The Big Green (7-0, 4-0 Ivy League), ranked 15th in the STATS FCS Top 25, managed only a 42-yard field goal by Connor Davis with 59 seconds left before halftime before Kyler's game-winning toss.
Jake McIntyre kicked a 41-yard field goal midway through the first quarter to give the Crimson (4-3, 2-2) a 3-0 lead. McIntyre's 38-yard field goal with 9:48 left in the third quarter gave Harvard the lead until the final play.
Kyler completed 11 of 18 passes for 133 yards with an interception. Backup Jared Gerbino connected on 11 of 16 passes for 88 yards and a pick. Dartmouth managed just 52 yards on the ground on 25 carries.
Devin Darrington rushed for 102 yards on 25 carries for Harvard, which finished with 134 yards on the ground. Jake Smith was 17-of-28 passing for 170 yards. The Crimson had a five-game winning streak at home snapped.
Harvard coach Tim Murphy will have to wait at least one more game to tie former Yale coach Carm Cozza's record of 179 career Ivy League victories.
Dartmouth has won two straight in the series after ending a 14-game losing streak to Harvard last season.
Dartmouth and No. 12 Princeton (7-0, 4-0) will meet with sole possession of first place on the line next Saturday at Yankee Stadium.
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