Subs used: Andrew Warwick for John Andrew (12 mins), Adrian Hamilton for Mulholland (25), Alan Smyth for McIlroy, Richard Aingworth for Fitzpatrick, Conor Carey for Shawe, Ian Vance for McBurney, Steven Dickey for Hamilton (all 72).
Subs used: Alan McMahon for Rael (28-30 mins, blood sub; 73), Peter O'Shea for Vaipulu (40+1-50, temp sub), Peter O'Shea for Lavery (50), Shane Buckley for Neville (47), Anthony Kavanagh for O'Gorman (51), Declan Lavery for O'Shea (55), Conor Hartigan for McKenna, Ian Hanly for Gaughan (both 68), James McInerney for Cusack (76).
The boot of Ulster's Luke Marshall gave Ballymena their slender advantage after a tightly contested, defence-dominated first half at Templeville Road.
Garryowen swooped for the opening try in the 24th minute when young scrum half Neil Cronin blocked down his opposite number Blane McIlroy.
But a succession of penalties at the breakdown cost the Light Blues, who had Declan Lavery and Corey Hircock sin-binned in quick succession before the break.
However, in captain Paul Neville's last game for the club, Garryowen's powerful pack and quick-witted half-backs Cronin and Fergal Lawlor gradually wore down Ballymena's challenge.
The strongly-built Gaughan cut through for tries after 46 and 60 minutes, and fellow winger Ronan O'Mahony added another as Paul Cunningham's men joined Cork Constitution as two-time winners of the All-Ireland Cup competition.
Neville issued a statement of his side's intent by clattering into Ross Hackey as the Ballymena number 8 received the kick-off.
The 2007 champions had the better of play in the early stages with David Sherry and Lemeki Vaipulu carrying strongly, although Ballymena's defence was very well organised.
Meaty tackles from Marshall and Callum Black kept Garryowen at bay and it was the Braidmen who edged ahead in the 14th minute, following a neat attack involving Marshall, Caolann Fitzpatrick and Simon Shawe.
Shawe drew an infringement at a ruck, straight in front of the posts, and Marshall had no trouble in slotting the central kick.
Facing into a difficult wind, Garryowen turned down a long range opportunity to reply after strong scrummaging from JP Cooney won them a penalty.
Declan Cusack's touchfinder set up a lineout maul and although Ballymena won turnover ball, teenager Cronin got a terrific block on McIlroy's attempted box kick from a ruck near the try-line and dotted down for an unconverted effort.
John Andrews' charges had an immediate chance to respond, however Marshall's difficult penalty attempt from the left failed to split the posts.
Garryowen used their maul to good effect and profited from a consistently strong scrum, retaining possession intelligently although scoring chances were at a premium.
Some over-eagerness at the breakdown led to frustrating penalties for both sides, as they tried to build through the phases.
Garryowen were guilty of overplaying the ball in their own half at times and a huge hit from Hackney on Neville forced a 38th minute penalty, yet Marshall could not find the target.
The Braidmen kept the pressure on as half-time approached, driving forward from a lineout and Garryowen prop Lavery was yellow carded for infringing at the maul.
A scrum was called for and as Ballymena swept the ball back towards the posts, centre Hircock was pinged for failing to release the tackled player and promptly sin-binned.
Marshall claimed three points from the close-in penalty, moving his side back in front and punishing Garryowen's indiscipline.
Neville and company had the wind at their backs in the second half, and out-half Lawlor was narrowly wide with an early drop goal effort.
Ballymena were reduced to 14 men when Hackney came in at the side of a ruck - although the ball looked like it had squirted out of Garryowen's control.
Patient build-up play from the Light Blues was then rewarded as they created an overlap on the left for Gaughan to crash over in the corner past three defenders.
Cusack was unable to add the extras but restored to their full complement, Garryowen began to dictate with the lion's share of possession and territory.
Lawlor kicked intelligently out of hand and it was his superb pop pass that invited Gaughan to hare through a gap and in behind the posts for a smashing score on the hour mark.
Cusack converted this time to widen the margin to 17-6 and Ballymena were struggling to stay in touch.
Starved of territory, the Ulster Senior Cup winners were unable to make an imprint on the second period as they faded out of the game.
Marshall and McBurney were willing runners and skipper Paul Pritchard produced another all-action display at the coalface, but Garryowen were now in the ascendancy with Cooney, Sherry and replacements Anthony Kavanagh and Shane Buckley all impressing up front.
And while Ballymena out-half Martin Irwin was in the sin-bin, Garryowen hammered the final nail in their opponents' coffin with a fourth try.
Cusack punched a well-weighted chip towards the left corner and the ball broke for O'Mahony to lunge over from a metre out. Replays showed that Hircock might have knocked the ball on before O'Mahony got to it, but the score stood and Cusack converted for a 24-6 lead.
It was all Garryowen at this point and it took some committed defending from this game Ballymena outfit to avoid leaking more points.
Cusack pushed a 75th minute penalty away to the right, and Vaipulu was held up over the try-line as the Light Blues went for the jugular.
Referee: Eanna O'Dowd (IRFU)