John Anderson also scored from his left wing berth, with the in-form Gareth Fry booting two conversions and a penalty for the victorious Belfast side.
Wanderers did have their spells of dominance but two Niall McNamara penalties were all they could muster.
Belfast Harlequins' former player-coach Andy Ward came back to haunt the club when he won the late penalty which steered Ballynahinch to a famous 16-13 victory at Deramore Park.
It was 'Hinch's first ever AIB League win over Harlequins and came late on when Ward, a second half substitute, drew the infringement which allowed Ryan Bambry kick the clinching goal.
With league points and provincial bragging rights on line, there was added intensity to this game. Both sides put in some tremendous tackles and 'Quins got a foothold in the first half to move 10-0 ahead.
The hosts' inside centre Keith Pyper was successful with a third-minute penalty to open the scoring.
After a nervy opening, 'Hinch settled but their New Zealand out-half Bambry missed a penalty shot and the pack was held up over the line on the half-hour mark.
As half-time approached, Harlequins grabbed a converted try when their impressive number 8 Chris McCarey charged over off the back of a five-metre scrum.
Ballynahinch coach Derek Suffern elected to bring on Ward and powerful prop Lewis Johnston for the second period and thoses switches paid immediate dividends.
A huge push off a five-metre scrum, five minutes after the restart, saw the 'Quins pack shunted back over their line and lock Gareth Rourke was able to dot down for the visitors.
It was quite a moment for Rourke, who previously played for Harlequins, and with Bambry converting, the gap was down to 10-7.
Harlequins looked dangerous out wide, but Ulster scrum half Paul Marshall was not getting the possession he wanted and in the areas that 'Quins could put their opponents under pressure.
'Hinch's scrum was their best weapon and this came to bear in the final quarter, after Pyper and Bambry had swapped penalties for 13-10.
Harlequins lost their discipline somewhat as Bambry kicked the sides level in the 74th minute and then, just three minutes from time, he brilliantly split the posts again from the ten-metre line after a 'Quins player was adjudged to have kicked out at Ward.
'Quins, for whom Pyper and second rows Alister Heatlie and Neil McComb starred, won back possession and mounted a late comeback but the game fizzled out, allowing 'Hinch to make history.
At Shannonvale Cross on Saturday, Greystones launched a thrilling comeback to beat hosts Clonakilty 14-13 and secure their first win of the league campaign.
By the 25-minute mark, Clon had chalked up a converted try from Derek Dillon and two penalties from club captain David Lombard.
But Greystones managed to turn the game on its head just before the interval. Two well-executed tries from Ronan Carroll and Dave McKechnie, both converted by influential out-half James Power, edged the Wicklow men in front.
And they stayed ahead throughout a dour second half. Power got closest to adding to the visitors' tally when his drop goal attempt drifted the wrong side of the posts.
After drawing with Lansdowne last week, UCC managed to open their win account at home to their Cork compatriots Highfield.
The students got off to a flying start when centre Scott Deasy and winger Colin Crowley combined well down the left, and after a one-two between them, Deasy popped a pass to his right for flanker David Daly to run in under the posts.
Out-half Gavin Duffy converted for a 7-0 lead after just five minutes' play. Highfield replied with a 23rd-minute penalty from former Ireland international Brian O'Meara.
UCC soon moved 14-3 ahead when scrum half and captain Sam Cronin sniped through on a 30-metre charge, he passed back to Daly who was able to put supporting lock Neilus Keogh over for a converted try.
The Highfield defence was unlocked again in the 39th minute when Cronin countered off a scrum and exchanged passes with Deasy before dashing over the line in the right corner and rounding in behind the posts.
Duffy added the conversion, which was cancelled out by an injury-time penalty from O'Meara.
UCC bagged the only score of the entire second half when winger Peter Shallow made a 60-metre burst to nab a fine individual try, which handed the students a bonus point and a winning scoreline of 26-6.
One of the most impressive displays of the weekend came at the RDS where Lansdowne hammered the reigning Division Three champions Instonians by 37-6.
South African recruit Charl Oosthuizen caught the eye once again for the Dublin 4 side. He scored all of their points in last week's 19-19 draw with UCC, and tallied up 17 against Inst.
Former Under-20 out-half Lorcan Kavanagh scored two tries for Lansdowne, while Oosthuizen, David Hewitt, a newcomer from Esher, and prop Darren O'Reilly also touched down in the bonus point success.
Johnny Watt kicked two penalties for Inst, who are winless and bottom of the table.
Table toppers Bruff enjoyed profitable first and final quarters to take an 18-16 verdict over Thomond in the sides' Limerick derby.
Out-half David Maw missed two penalties for Bruff before his half-back partner Joe Lyons tapped a penalty and sliced through for the game's opening try, 16 minutes in.
Brian Cahill tagged on a subsequent penalty for 8-0 but Thomond dug their heels in and succeeded in reducing the arrears to just two points by the interval.
Declan Cusack kicked two penalties from four attempts to get Thomond into the game and hand them a slight psychological edge for the second half.
Cusack booted the visitors into a 9-8 lead, eight minutes after the restart. Thomond were beginning to get on top but the Bruff defence held firm.
However, the home side lost number 9 Lyons to the sin-bin and suffered another setback when Brian Cahill, who had taken over the kicking duties from the departed Maw, missed a penalty.
Cahill redeemed himself by landing a 70th-minute effort for 11-9 and Bruff enjoyed a purple patch, with Peter Malone, captain Cathal O'Regan and Martin O'Rourke all leading from the front.
Still, Thomond were particularly dangerous in open play and when Cusack quickly turned an intercepted pass into a kick chase, Bruff were in trouble.
Left winger Dara O'Neill won the race to the ball to notch Thomond's second try and at such a crucial stage, with only eight minutes remaining.
Cusack's conversion left his side 16-11 ahead but incredibly, Bruff had another spurt in them. Their pack quickly regained possession and set up camp near the Thomond line.
Although time was running out, O'Regan and his men showed great composure and their persistence paid off when Malone got over for a last-gasp try off a five-metre scrum.
Brian Cahill stepped forward to kick the conversion and the two-point buffer was enough to seal another memorable win for the Division Two newcomers.
Credit must go to Thomond for making it such a super-charged and drama-filled game, in which neither side deserved to lose.
Meanwhile, Old Crescent and Dublin University shared out four tries in an entertaining encounter at Rosbrien on Saturday.
The Limerick side claimed a 19-13 win thanks to unconverted tries from Arron Carroll and Emmet Dalton and penalties from new out-half Brian O'Shea (2) and Mark Woods.
The one game to take place on Sunday went the way of Bective Rangers, who outlasted DLSP for a 36-23 triumph at Donnybrook.
AIB League Division Two Results
AIB League Tables
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