Frazier, who entered the game third in the Big Ten in scoring at 19.1 points per game, went just 1 for 4 from the floor in the opening half before scoring 15 points in the final 13 minutes to lead the Nittany Lions (6-2) to the win.
Matt Humphrey led Boston College (2-5) with 15 points and Gabe Moton had 10. The Eagles were 5-0 in ACC/Big Ten games before the loss.
Frazier's 3-pointer from the top of the key pushed Penn State ahead for good, 51-48, with 6:59 to play.
The Nittany Lions certainly didn't pull away, though, as the Eagles closed the gap to two points twice. But BC never had a possession when it could tie or take the lead.
Penn State put it away with free throws in the closing minute.
The second half started like many stretches of the sloppily played game: with turnovers and missed shots. Each team turned the ball over twice in the initial four possessions after the break.
Penn State, which trailed by three at intermission, took the lead, 32-31, when Frazier scored 5 straight points, including a 3-pointer from the left wing that pushed the Nittany Lions ahead with 17 minutes to play.
After BC's Dennis Clifford hit two free throws, Lonnie Jackson nailed consecutive 3s just 33 seconds apart during a 9-0 run that gave the Eagles a 38-32 edge with 14 1/2 minutes to go.
The Nittany Lions tied it 42-all on Frazier's 3-pointer from the top with 10:12 left. He tied it again at 46 with two free throws with just 9 minutes to play.
In the first half, the Eagles took advantage of Penn State's poor shooting and led 29-26 at intermission. The Nittany Lions shot just 36.7 percent in the opening 20 minutes, going 4 for 14 on 3-point attempts.
Without Marshall's scoring it could have been much worse for Penn State. He scored 15 points on 6 of 9 shooting, establishing a new season-high in the first 20 minutes.
The Eagles weren't that much better, hitting 45.5 percent and going 4 for 13 on 3s.
BC pulled to a 12-4 lead in the game's opening 4 1/2 minutes, with KC Caudill scoring its first 6 points. The Nittany Lions, who missed their first six shots from the floor, then scored the next 10 points before the lead switched hands five times over the final 12 minutes of the half.
Penn State started off slowly like in its last game, a loss at St. Joes Saturday. The Nittany Lions missed their first 16 shots from the field and fell behind 22-0 en route to a 65-47 defeat on Saturday.
See the box score here: