The game had finished 17-17 after 80 minutes of play in what had been a superbly contested final played in ever-changing weather conditions at Kingspan Stadium.
It was Malone who struck first when influential captain Peita McAlister combined well with scrum-half Shirelle Wilson, before releasing number 8 Lauren Maginnes to score the first try of the game.
QUB replied and made it 5-5 through fullback Alexandra McIlwaine who was sent clear through a gap in the defence after good hands from her captain Ciara Grogan.
Malone ramped up the pressure after Queen's winger Abby Sheridan saw yellow for a high tackle, and they quickly made the most of their advantage.
McAlister found Emma Jordan inside the 22 after the outside centre had run a brilliant line to slice through the defence and race clear to touch down under the posts, with Grainne Murphy converting to give them a 12-5 lead at the break.
On the other side of half time, another try from Malone's Maginnes looked to have got her side one hand on the trophy, but QUB rallied from 17-5 down to pull level.
Scrum-half Rachael McIlroy did well to release replacement Emma McArdle down the left wing before collecting the return pass to finish under the posts, with Diane Ramsay adding the 2 points.
They then got themselves level with a sensational late try from McArdle. A turnover at the breakdown saw the ball work its way back into her hands, and she ran in from well inside her own half, beating several defenders on her way to the whitewash.
It meant the game ended 17-17 after 80 minutes, which set up two periods of extra time of 10 minutes each. Both sides were well matched and the game could have gone either way, but Malone kept QUB under pressure and camped inside their own half.
Eventually this pressure told and Malone were awarded a penalty just inside the 22. Up stepped Grainne Murphy, with her kick splitting the posts and securing 3 vital points which proved enough to win the final.
