Mahut, who won his first career ATP title in the Netherlands last month, added a second in quick succession after a marathon day in Rhode Island.
He beat American Michael Russell 6-2 6-2 in their rain-delayed semi-final in the morning then returned to the grass court to defeat Hewitt 5-7 7-5 6-3 in the afternoon final.
The Australian, bidding for his first singles title since he beat Roger Federer in the final at Halle in June, 2010, also played in the morning, blunting the booming serve of twice defending champion John Isner to win 5-7 6-2 6-4.
Despite spending more than an hour longer on court in his semi-final, the 32-year-old Hewitt looked to be on the verge of a straightforward victory in the final.
He won the opening set then served for the match at 5-4 in the second set but was unable to close it out as Mahut, a runner-up in Newport six years, fought back.
Mahut, 31, won the next three games in a row to force the match into a third set and despite going down an early break, he recovered and went on to seal victory after two hours and 20 minutes.
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