Jaffray scored on the power play in the first period, again at the 18:15 mark of the third, and an empty-netter with 50 seconds left to seal the hat trick.
Manitoba head coach Scott Arniel was impressed that his club wasn't down after Grand Rapids forward Scott Parse scored a third-period goal to tie it 1-1.
"I like the fact that they didn't get rattled and we just continued to push forward," he said. "For two tough pressure situation games we really were composed and all 20 guys played solid."
Moose blue-liner Yannick Tremblay, who was recently called up to the Vancouver Canucks to play in their NHL playoff series against the Anaheim Ducks, scored the eventual winner in the third period and added two assists.
"Tremblay came up with the big shot with five minutes left," said Jaffray about his teammate. "I don't know how it went in, but that was our game plan on Jimmy Howard to throw pucks from everywhere because he doesn't get caught out of position too often."
Brad Moran also chipped in with two assists for the Moose.
MacIntyre stopped 21 of 22 shots, while Griffins netminder Jimmy Howard turned aside 31 of 34 shots.
Manitoba will now meet the Hamilton Bulldogs in a best-of-seven series that starts Saturday night in Winnipeg.