Baker trailed by as many as nine points with 4:08 to play but continued to dig into that lead with a bucket by Todd Eils to cut the lead to seven, 64-57.
Eils then cut the lead to just four with 2:22 to go with a bucket at 65-61. Rustin Dowd then made one free-throw to put MNU up five. Baker's EJ Carter then knocked down a basket in the paint to cut the lead to three, 66-63.
With 46 seconds left senior Jordan Honore went to the free throw line with Baker down 67-65.
He missed the first of two, then made the second to put Baker down one, 67-66. Honore went down the floor on Baker's next possession and knocked down a jumper with eight seconds left to give the Wildcats its first lead since the 3:16 mark in the first half.
But MNU went down for the floor for one final shot and Jacob French knocked in a bucket in the paint right before the buzzer sounded to advance the Pioneers into the HAAC Semifinals.
The Pioneers will now take on No. 2 seeded Culver-Stockton on Saturday afternoon. With the win MidAmerica improves to 23-8 on the year, while Baker ends its first season under head coach Sean Dooley 15-14.
Second-Team All-Conference performer Ben Steinlage led all scorers with 16 points and was nearly perfect from the free throw line, shooting 8-of-9 and teammate Corey Anderson was perfect from the line on 10-of-10. In fact, the Wildcats kept themselves in the game with their outstanding free throw shooting, 85.7-percent on 24-of-28.
Baker dominated the boards, outrebounding the Pioneers, 32-23 and allowed just four MNU offensive rebounds. They also held the Pioneers to just 11.1-percent from behind the arc, on 1-of-9.