The Garryowen pack were excellent throughout the derby encounter with Shannon - hooker Damien Varley, lock Mark Melbourne and replacement flanker David Sherry were amongst the players to stand out for the defending Division One champions.
They needed to show plenty of resolve as they lost their openside and captain Paul Neville to a shoulder injury, midway through the first half.
But, 14-3 ahead at the break, Dara O'Sullivan's charges found an extra gear playing into the wind in the second period, with tries from Kieran Lewis, Conan Doyle and Keith Earls sealing a famous victory.
Malone typically led from the front, throwing himself into tackles and securing phase after phase of possession through his tireless work at the breakdown.
The AIB Club international forward is in his seventh and final season at Dooradoyle having tied up a move back to his native Bruff as the Division Two side's player-coach.
With a league final to look forward to next Sunday against Cork Constitution, the former skipper was delighted with how Garryowen performed against Shannon.
"We knew we had to restrict Shannon in the first ten minutes of the second half. They got three points back but once they didn't get a try we knew we were comfortable enough.
"We knew we had the pack to hold onto to the ball in the conditions in the second half - and we did that for the middle 20 minutes of the second half which was the most important part," he said.
After losing two of the three titles they won so impressively last season, Garryowen were determined to stay in the league title race and coach O'Sullivan had them playing to the right gameplan at Coonagh.
"(At half-time) Dara just said we have to keep playing. We were 11 points up. You can't sit back on a lead against Shannon cos Shannon will always come back at you," Malone added.
But the former Ireland Under-19 and Under-21 international felt that the 25-point winning margin was somewhat flattering to the visitors.
"The score wasn't really a reflection of the game. Shannon have a great record in play-offs here in all competitions. I've never personally beaten Shannon in the semi-final or a final of any cup.
"So to beat them in the semi-final of the AIB League is a great feeling but the score-line is kind of irrelevant."
Malone is expecting a fierce battle with Cork Constitution when the sides meet in next Sunday's televised final at Musgrave Park (kick-off 1.15pm).
Con lost 16-15 in last year's decider at the same venue and the sides shared the spoils with a 12-12 draw at Temple Hill in the league proper in November.
"It will be a tough ask (for us). We've played Cork Con two or three times in the last two years and there's never been more than two or three points between the teams over the course of those games.
"We drew this year, there was a point between us last year so it's going to be another tight game."