The Pipers (9-12, 8-8 in the MIAC) moved into a tie for fifth place in the conference with the victory.
Thrasher hit his first five shots from the field during the first half as the Pipers took a 39-22 halftime lead. Hamline shot 56 percent in the first 20 minutes.
Leading 15-14 with nearly eight minutes left in the first half, Hamline went on a 15-4 run to take command of the game. Six different Pipers scored during the spurt.
Hamline would take a 17-point lead into the break when Thrasher hit a three-pointer as time expired.
The Pipers pushed the lead to 59-33 midway through the second half before the Auggies (3-18, 2-14) made a comeback.
Thrasher led four Pipers in double figures. Senior Charley Good added 13 points. Junior Kyle Foster had 11 points and 13 rebounds, while Ryan Montgomery came off the bench to score 10.
The Pipers shot 54 precent in the game (29-54) and went 24 of 35 from the free throw line.
Augsburg was paced by Devin Rose's 13 points. Justin Kozlowski and Charlie Scott each added 12 points, and Kevin Keto chipped in 11 points.