The 17 penalties for 159 yards were believed to be Dartmouth records.
The Lions (1-5, 0-3 Ivy), losers of 26 of their last 27 games, gave the Big Green (6-0, 3-0) a game before falling to Dartmouth for the seventh consecutive time. Dartmouth is off to its best start since 1997.
Dartmouth, playing as a ranked FCS team for the first time in 19 years, needed its stingy defense, ranked third nationally at 9.4 points per game. The Big Green rushed for a season-low 88 yards but held Columbia to 61 on the ground and 167 overall.
Dalyn Williams threw a 5-yard touchdown pass to Victor Williams in the second quarter for a 13-3 lead.
Charlie Miller's first interception, at the Dartmouth 39, with under a minute left sealed the win.