The world number 17 earned a 6-7(4) 6-4 6-4 victory at the age of 32 years and 11 months in the last final to be held at Crandon Park.
After losing the opening set Isner battled back to prevail in a time of two-and-a-half hours for his maiden title, having previously finished runner-up at Indian Wells in 2012, Cincinnati in 2013 and Paris two years ago.
Both players held their serve throughout the opener, but it was Zverev who took the tie-break after claiming four points on the spin.
Isner again held in the second set and earned the only break in the ninth game to level up the contest, before doing likewise in a replica third set.
The American is the first player ranked outside the top 10 to lift the trophy since 1991.