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.
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 a goal and two assists for the Moose. Brad Moran chipped in with two assists.
Forward Scott Parse scored a third-period goal for Grand Rapids to spoil Drew MacIntyre's shutout bid.
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.