Auger-Aliassime, 18, has been the surprise package of the week in Florida, the qualifier having not dropped a set since the second round.
But the final proved a step too far, as Isner - yet to drop a set in the tournament - battled through to a decider against Roger Federer or Denis Shapovalov.
Auger-Aliassime struck the first blow when he broke the Isner serve to go 4-3 in front, but Isner hit back three games later to force a tie-break.
Isner dropped his first two service points in the breaker but Auger-Aliassime did too and the former turned it around to edge in front.
The American then fell behind in the second set, too, but once again Auger-Aliassime could not make the advantage stick.
On this occasion, Isner won the first point of the tie-break on his opponent’s serve, which proved enough to wrap up a win that ensures he will remain in the world’s top 10.
Victory in the final would see Isner move from ninth to eighth in the rankings.
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