VMI rallied behind freshman forward Reggie Williams and returning starter Sam Mielnik to outscore Navy12-2 over the next two minutes and cut the lead to just three (29-26) with 5:39 to play.
Though VMI took the lead in the first half, Levar Joseph's bucket with 3:18 to play knotted the game for the fourth time at 32-32.
Freshman forward Carlton Baldwin (Lusby, Md.) came off the bench to see his first minutes of the season, scoring a bucket with 2:59 to go and a free throw by Mergerson gave Navy a three-point lead. VMI's Matt Murrer connected on a jumper with 27 seconds to play to put the Keydets to within one at the half, 35-34.
The opening seven minutes of the second half featured back and forth scoring by both teams. Navy opened an eight-point, 56-48 lead on a pair of buckets by junior forward Matt Fannin (Lakewood, Ohio) and a three-pointer by Taj Mathews (Mercer Island, Wash.) with 12:10 to go in the contest.
Over the next 10 minutes, the Keydets outscored Navy 23-7 to take a 71-63 lead with just under two minutes to play.
Fannin's old-fashioned three-point play, along with a triple by Mathews and a jumper by senior forward George O'Garro (Panorama, Calif.) narrowed the gap to just one point at 72-71 with 1:04 to play.
VMI's Preston Beverly tipped in a bucket with 29 seconds to play to give the Keydets a three-point lead, followed by a missed three-pointer by Hooper which left Navy with little choice other than to foul.
The Keydets knocked down all four free throws in the last 15 seconds to earn their second win of the season.
Though Navy outboarded VMI, 52-41, the Mids were hurt by their 22 turnovers. The Mids also shot just 11.5 percent from long range, making just three of their 26 triples.
Despite the loss and struggles in the three-point shooting column, first-year Navy head coach Billy Lange was optimistic about the game and season.
"We played better than the games against the Merchant Marine Academy and Loyola," said Lange. "We're a team still learning to maintain focus. I like where we are headed and that's the most important thing.
"We lost our hustle and energy down the stretch and got beat to some 50-50 rebounds at the end," Lange added. "We pride ourself on our defense and down the stretch, our focus faltered a bit."
Fannin had a strong effort for the Mids, posting his first-collegiate double-double with career highs in scoring (20) and rebounding (13). He shot 60 percent (6-10) from the field and 72.7 percent (8-11) from the free throw line. Mathews also had a career day in the scoring column with 19 points, while adding a team-high four steals and three assists. Mergerson, who sat out the final 15 minutes of the contest after suffering a laceration above his eye, added 10 points, five rebounds and three blocked shots.
VMI was led by Joseph's 18 points, which included four three-pointers. Starting guard Matt Coward scored 12 of his 16 points from the free throw line, while Williams added 14 points and a team-high tying six rebounds.
Navy returns to action Wednesday when it plays host to Morgan State. Action is set for 7:30 p.m. at Alumni Hall.