Penn ended its season at 11-4.
"This is amazing," said Saputo, a midfielder from Huntington, N.Y. "As a group, this was our goal - to win the CAA and carry on to the NCAA tournament. And it's surreal and we want to keep it going."
The Dragons scored three goals in the final 17 seconds of the second quarter and the first four of the third.
"They scored seven straight, and that made the difference in the game," Penn coach Mike Murphy said. "We never really recovered, and a lot of that was due to their faceoff guy."
The last two Drexel goals in the second quarter came from Saputo, who won the faceoffs and then went down to score both times. That gave Drexel a 7-6 halftime lead.
After his late flurry in the second quarter, Saputo continued to have success on faceoffs in the third period, winning five of six. It helped the Dragons take an 11-7 lead into the fourth quarter.
For the game, Saputo was successful on 21 of 30 faceoffs (70 percent). He entered the game ranked fifth in the nation with a 63.2 winning percentage.
"I thought Penn totally outplayed us in the first half," said Drexel coach Brian Voelker, who coached Penn for seven years before taking over the Dragons program in the fall of 2009. "I was hoping we could go into halftime maybe only down one, and [Saputo] turns the thing around and made the momentum go from one side to the other."
Ben McIntosh also scored three goals for Drexel, all in the fourth quarter. His third goal was his 46th of the year, setting a single-season school record.
Jules Raucci, a sophomore from Garnet Valley High, had two goals and two assists for a team-high four points. Goalie Will Gabrielsen made several big saves and finished with 12.
Sophomore Nick Doktor led Penn with three goals.