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.
Georgia coach Kirby Smart: 12-team playoff would be college football's 'greatest change'
Georgia's Kirby Smart, LSU's Ed Orgeron and Coastal Carolina's Jamey Chadwell all shared their thoughts on the possibilities of an expanded College Football Playoff.
Ex-Colorado QB Sam Noyer heads to Oregon State for final season
Former Colorado quarterback Sam Noyer will use his final year of eligibility at Oregon State.
College Football Playoff expansion: 12-team historic simulations, storylines and more
Bill Connelly crunches the numbers using SP+ to figure out the most likely scenarios for how a 12-team playoff would have played out since 2014.
Latest on Bo Schembechler ignoring warnings of sexual misconduct from doctor
Michele Steele reports on claims that the late Bo Schembechler ignored warnings about former team doctor Robert Anderson's sexual assaults.
Herbstreit calls CFP expanding to 12 inevitable and for the best
Kirk Herbstreit joins SportsCenter to discuss the College Football Playoff possibly expanding to 12 teams.
Former Michigan football players say coach Bo Schembechler ignored warnings, son's complaint about doctor's abuse
Former Michigan football players Dan Kwiatkowski and Gilvanni Johnson, who have told investigators they were molested by former team doctor Robert Anderson, said head coach Bo Schembechler ignored their warnings at the time about abusive treatments.