Despite the end result, the Wildcats dominated the match offensively with 20 shots taken and 14 on goal, compared to five shots and three on goal for the Spartans.
MBU's goalkeeper John Schnurbusch had an impressive 13 saves on the night, while Ryan Emme had two for BU.
The Spartans got on the board first with a goal by Jamie Skillen in the 53rd minute. Skillen's goal was one of the most difficult and spectacular goals you will see all season, as he lifted the ball from 50 yards out at midfield and sent it right over the finger tips of Emme for a goal.
Keaton Anchors led all players with five shots and tied things up for BU with 18 seconds to go in the second half to send the game into OT. Sophomore Spencer Atkin earned the assist.
Six players had two shots for the 'Cats including Amer Didic, Chris Tuso, Spencer Atkin, Robert Hoeven, Blake Levine and Jordan Thacker.
The Wildcats will next take on No. 4 ranked Ashford on Saturday afternoon also at Liston Stadium for a rematch of the NAIA Round of 16 game from a year ago.
Ashford ended Baker's season 3-2 in double overtime last year in Montgomery, Ala., in the NAIA Men's Soccer National Championship final site.
The match can be found live on www.bakerwildcats.com via live stats and live video.