Gordon's 26-yard touchdown run tied the game 7-7 in the first quarter and Scales' 46-yard score in the second put the Crimson (4-2, 2-1 Ivy League) ahead 14-7.
After going three-and-out on three straight pass plays on its first possession, Harvard gained 394 rushing yards.
Collier Winters, who was injured for Harvard's first five games, started the second half and threw two touchdown passes.
Andrew Kerr had two touchdown catches for the Tigers (1-5, 0-3), the first on a 22-yarder from tight end Harry Flaherty. The other was thrown by Andrew Dixon, who was 20-for-29 for 195 yards but was intercepted twice.
Princeton leads the venerable series 53-43-7 but Harvard has won 13 of the past 15.
Kevin Weidl and Marcus Spears look at the best fit, biggest surprise and best player left from the SEC after the first round of the 2016 NFL Draft.
13 minutes before the draft began, Laremy Tunsil's Twitter account was reportedly hacked and a video of Tunsil smoking surfaced. The drama didn't end there as the 13th overall pick dominated the headlines on draft night.
SEC Network checks into Mississippi State's spring football practice for a sneak peak at their offseason adjustments.
Kevin Weidl and Marcus Spears look at how former Ole Miss players Laquon Treadwell and Robert Nkemdiche will fit with the Vikings and Cardinals, respectively.
SEC Network's Peter Burns talks with Seattle Seahawks' 31st overall pick Germain Ifedi about the feeling of being drafted and his excitement for Seattle.
SEC Network's Peter Burns talks with Indianapolis Colts' 18th pick Ryan Kelly about his experience in the NFL draft and thoughts on playing in the NFL.