Harper led four players in double figures, as Max Landis added 16 and Jerome Hill and Tyler Strange each netted a season-high 11 in the win. Landis joined Harper on the All-Tournament squad.
"I am unbelievably proud of our kids," said Gardner-Webb head coach Chris Holtmann. "To have this schedule for the past week and play what I think is our cleanest and most sound game is a credit to our kids and their toughness.
"Austin Peay is a very good, very well coached team. They will have a good year. I'm just really happy four our kids to win this championship."
Gardner-Webb (4-3) found itself down 29-27 at the half after Austin Peay (2-3) got hot from long distance in the final two minutes before the break. The Govs knocked in 5-of-10 shots from long range in the half to overcome another strong defensive lockdown by the Runnin' Bulldogs.
The deficit marked the first time Gardner-Webb has trailed at the break since the season opener at No. 11 North Carolina.
The two teams battled evenly over the first five minutes of the second half, and Austin Peay's Will Triggs converted a conventional three-point play with 14:04 left to put the Govs up 42-38.
A put back by Hill cut the lead to 42-40 on Gardner-Webb's next possession, and Landis drilled a three from the left wing to put the 'Dogs up for good, 43-42, with 12:49 left.
Gardner-Webb would slowly pull away, going on a 19-7 spurt to lead 59-49 on back-to-back jumpers from Landis with 8:22 to play. Landis and Harper combined to score 11 of GWU's 19 points in the rally.
A pair of treys from Austin Peay quickly tightened the game, however, with Travis Betran and Anthony Campbell knocking in consecutive bombs to make the score 59-55 with 6:49 left.
Strange answered with a three from the left wing at the 6:25 mark to stem the tide, but Betran followed with another three-pointer with 5:24 left to pull the Governors within four points.
After Will Triggs worked free for a layup to pull Austin Peay within 65-62 at the 2:49 mark, Strange took over. The 5-foot-9 lead guard shook a pair of Governors late in the shot clock for a driving layup off the glass for a 67-62 lead, and repeated the move with 1:16 left for a 69-62 lead.
Strange then iced the game with two free throws in the final 30 seconds.
Gardner-Webb shot a strong 51.6 percent in the second half (16-of-31), made 4-of-9 from deep after the break (44.4 percent) and wound up at 45.2 percent from the floor for the game.
The Runnin' Bulldogs held a remarkable 46-30 edge on the backboards, with Harper and Hill each fighting the taller Governors for eight apiece. Harper added four assists and a steal in another strong floor game.
Tashan Newsome saw his first action in more than a week, playing limited minutes off the bench - but toughing his way to six points, six rebounds and a pair of assists in 15 minutes.
Austin Peay shot 40.4 percent for the game, and cooled off from long range in the second half to shoot 8-of-21 from that distance over 40 minutes (38.1 percent).
Betran scored 12 of his team-high 18 points in the first half and center Chris Horton added 10 points and four blocks to pace the Govs.
Gardner-Webb will return home on Thanksgiving Day before hitting the road gain for a Sunday game at surging Big Ten program Illinois. That game is set for 4:00 and will be televised on the Big Ten Network Sunday afternoon.
Donta Harper, Gardner-Webb (MVP)
Max Landis, Gardner-Webb
Travis Betran, Austin Peay
Chris Horton, Austin Peay
Trey Sumler, Western Carolina