Michael Alvarado had 14 points for Manhattan (14-18). The Jaspers led for much of the game and were up by five in the second half before Manhattan went on a 17-2 run to take charge.
This is the Gaels’ eighth MAAC title but first since 2006. The victory also gives Iona 20 wins for the fourth consecutive season.
Manhattan led at halftime and was up 35-30 in the second half before Iona went on its run. Sean Armand’s layup gave the Gaels their first lead of the half at 37-35 with just over 13 minutes left.
Armand picked up his fourth foul just over a minute later, sending the team’s second leading scorer to the bench. Iona then put the ball in Jones’ hands and his off-balance jumper made it 43-37.
Manhattan coach Steve Massiello then picked up a technical foul after two warnings for coming out on the court. Jones hit the free throws, and Taaj Ridley extended the lead to 47-37 with a pair of foul shots.
But Ridley was forced to take a seat on the bench when he picked up his fourth foul with more than 8 minutes left.
Manhattan cut the lead to six on a steal and layup by Emmy Andujar with 2:30 left, forced a shot-clock violation and made it a four-point game on a pair of free throws by Rhamel Brown.
But the Jaspers could not get a rebound on the other end. A pair of foul shots by Bowman made it 58-52 and a steal and dunk by David Laury sealed it.
The game was played at Manhattan’s pace. Iona came in averaging more than 81 points, while the Jaspers were holding opponents to just under 61.
Manhattan missed its first six shots, but Iona made just two of its first seven and led 4-3 at the first media timeout.
The Jaspers used an 8-0 run to turn an 18-13 deficit into a 21-18 lead and quickly pushed it to six, but a jump shot by Jones just before the halftime buzzer cut the lead to 26-24.
Iona is hoping for some redemption after the Gaels wasted a 25-point lead in a first-round loss to BYU in last year’s NCAAs.
The New York rivals, whose campuses are separated by less than 10 miles, were meeting for the 82nd time but had never met in the championship game. They split two meetings during the regular season, including a double-overtime thriller won by Manhattan at home on Feb. 14.
The Jaspers had won eight of their last 10 coming in, and the two losses were by a total of four points.
Manhattan made its run to the final without its best player, guard George Beamon, who played just four games this season after suffering a severe ankle injury in the season opener.
Jones came in averaging 23.5 points, second behind Virginia Tech’s Erik Green on the list of the nation’s top scorers. But the MAAC player of the year has been fighting flu-like symptoms throughout the tournament.
Iona knocked off fifth-seeded Canisius and No. 1 seed Niagara on its way to the final. Manhattan upset third-seeded Loyola before beating seventh-seeded Fairfield.