Replacements used: Sean McCarthy (Shannon/Munster) for Thornbury (11-15 mins, blood sub), Ryan Furniss (Worcester Warriors/Exiles) for Taylor (31), McCarthy for Donnan (58), Josh van der Flier (UCD/Leinster) for Timmins (60), Adam Boland (Lansdowne/Connacht) for Furness (72), John Andrew (Ballymena/Ulster) for McGuigan, Darren Sweetnam (UCC/Munster) for Scannell (both 74). Not used: John Creighton (Malone/Ulster), Eogháin Quinn (Lansdowne/Leinster).
Replacements used: Nathan Morris (London Wasps) for Hobbs-Awoyemi (half-time), Nathan Fowles (Sales Sharks) for Day (49 mins), Harry Wells (Leicester Tigers) for Conlon, Tom Collins (Northampton Saints) for Purdy (both 68), Danny Herriott (Northampton Saints) for Wilson (70), Tom Jubb (Saracens) for Stooke, Will Hooley (Northampton Saints) for Slade (both 78). Not used: Max Crumpton (Saracens).
England had been on course for their second victory of the Championship with Henry Slade's trusty left boot banging over five excellent penalties from five attempts.
The visitors had lost their blindside flanker Ross Moriarty to a red card in the 23rd minute - he flipped Luke McGrath in a dangerous tackle - but their powerful seven-man pack, allied to Slade's scoring ability, had them leading 15-6.
With both sides losing their discipline at times, Daly and Athlone's own Robbie Henshaw saw yellow for Ireland in the second half and English lock Elliott Stooke also spent time in the sin-bin.
Winger Scholes kicked Ireland's third penalty while Daly was off and towards the end of Stooke's sin-binning, Mike Ruddock's youngsters struck for the only try of an error-strewn game.
Their best spell of continuity, with captain McGrath at the centre of it, pulled England wide to the right before play was swung to the opposite side where Daly and Henshaw combined and the Connacht full-back sent Scholes over close to the corner.
Daly added the extras under immense pressure for a 16-15 turnaround and the Irish scrum held its own in a tense final few minutes, with a final penalty allowing McGrath to gleefully kick the ball dead.
England will feel hard done by as Moriarty's dimissal seemed to spur his forward colleagues on, their hard work laying the platform for Slade's unblemished display of goal-kicking.
But Ireland's never-say-die attitude saw them doggedly stick to the task and they got their reward in the end, handing England their third defeat in four Under-20 trips to Athlone.
Speaking afterwards, Electric Ireland man-of-the-match Tom Daly said: "(With the conversion kick) I just tried to blank everything out. I've done it in training. I treated it like it was just another kick and thankfully it went over.
"We knew we could beat England. We talked about it all week, we’ve beaten them as Under-18s and Under-19s. We didn’t talk much about the sending-off, we just knuckled down and got on with it.
"Our pack really fronted up. They were amazing again, like they were last week (in Wales). The Six Nations is all open again, and hopefully we're back on the road to the Championship."
England edged into an early lead at the midlands venue, out-half Slade slotting a second minute penalty after the hosts failed to release on the ground.
Rory Scannell, deputising for the injured Steve Crosbie at out-half, hung up an excellent restart kick as the Irish pack gradually grew into the contest.
Peter Dooley was in the thick of the action during two solid opening scrums, and fellow new caps David Panter, Henshaw and Mark Roche also did well with early possession.
Scannell rifled away a fine touchfinder to the left, giving Ireland good territory as they pressurised the lineout throws of England's converted hooker Luke Cowan-Dickie.
A Daly run drew a kickable penalty on the quarter hour mark, but the big Lansdowne centre pushed his effort to the left and wide.
Henshaw and busy scrum half and skipper McGrath increased their influence with some tidy ball handling, and a smart break from Daly brought Ireland over halfway.
Both sides maintained a high level of physicality, however the error count made for a stop-start first half and there was also a hold up as McGrath received treatment having been upended by Moriarty.
Referee Nigel Hennessy brandished his red card, leaving England down to 14 men for the remaining hour. McGrath was fit to continue and Daly converted the resulting penalty from in front of the posts, drawing Ruddock’s side level at 3-3.
England responded well, Cowan-Dickie crashing the ball up and Slade landing his second successful penalty in the 29th minute.
He added a third four minutes later as Ireland conceded a couple of penalties in quick succession. A neat backhanded pass from McGrath to Ryan Murphy was the highlight of Ireland’s spirited response.
9-3 down at the break, Ireland clawed back three points in the opening minutes of the second half, Daly rewarding good work from the forwards and the threatening Scholes.
Scannell was unfortunate to see a kick go the wrong side of the corner flag, allowed England the possession and territory to set up a cracking long range strike from Slade.
Daly gobbled up the restart and Scannell weaved into the English 22 as the home side tried to answer back in the very next phase.
England upped the tempo as the final quarter loomed. Slade miscued a drop goal effort from long range, with his well-drilled pack proving a much better platform.
Pressure on the Irish defence saw Daly go off his feet at a ruck and earn a yellow card. Slade then managed to split the posts from the right and the gap was out to nine points.
Worse followed for Ireland as they were reduced to 13 players after Henshaw, chasing his own garryowen, took his opposite number Ben Howard out in the air.
The penalties continued to come, Ireland piling forward with lock Gavin Thornbury to the fore. Scholes crowned the attack with a well-struck penalty which visibly lifted the hosts.
England suffered a sin-binning shortly afterwards as Stooke was pinged for bring down an Irish maul illegally. Suddenly, the green shirts were driving forward again - the returning Henshaw and excellent number 8 Conor Joyce spearheading a break out of their own half.
The extra numbers told as Daly sniped in the England 22 and the forwards made good ground on the right as Ireland upped the pace under McGrath's baton.
Changing direction, Daly was found in midfield and he popped a lovely pass for Henshaw to continue the move and with England caught for numbers, Scholes had enough space to dot down and make it a one-point game.
Ireland completed their dramatic comeback with Daly's classy conversion and a disciplined spell of defending in the dying minutes.
The result marks Ireland's second successive win over England at this age grade, following on from last June's 27-12 IRB Junior World Championship play-off success in Cape Town. McGrath was the only player to line out in both matches.
Referee: Nigel Hennessy (Wales)