Germishuy's try had given the Eagles an eight-point lead with 20 minutes still to play, but they held on until after the fulltime hooter when Dougie Fife scored Scotland's fourth try.
Blair Kinghorn and George Turner had both scored first half tries for the visitors, while they were also given a penalty try to give them a comfortable 19-6 lead with halftime approaching.
Taufete'e, however, scored his first try less than two minutes later to give his side some momentum they continued after the break with his second five-pointer.
MacGinty's third penalty in the 47th minute gave the home side the lead for the first time.
The U.S. face Canada next week, while Scotland travel to Argentina to face the Pumas.
(Reporting by Greg Stutchbury in Wellington; Editing by Amlan Chakraborty)
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