Desperate to give his team an advantage, Ted Donato was forced to pull Mitchell Gibson with about 5 minutes to play but the ploy worked.
RPI managed to score their only goal of the game late in the third but it was not enough to overcome Harvard's lead and the Crimson escaped with a series victory.
By the start of the third period it appeared that Harvard was going to be sunk by taking bad penalties, but their top line surged in the final frame.
Nick Abruzzese, Matthew Coronato and Sean Farrell, who had already combined for five points, spearheaded the Crimson comeback and scored three goals in the third.
While the team took two more penalties, their defense held and stopped Clarkson from replying, sending the Crimson to the conference title game.
The team's offense was severely limited in scoring opportunities, recording just 12 shots in regulation to Quinnipiac's 42, but the Crimson were able to get two past Yaniv Perets and push the game into overtime.
The Crimson looked like they were going to be swept out of the building until Sean Farrell fired a puck from behind the goal line that deflected off of Dryden McKay and into the net.
After forcing the Mavericks into a penalty in the final 5 minutes, Gibson was pulled and Casey Dornbach scored on the ensuing two-man advantage.