Seniors Ben Steinlage, Corey Anderson and Jordan Honore all scored a team high eight points to help Baker improve to 15-13 overall and 8-10 in the Heart of America Athletic Conference.
The sixth-seede Wildcats will next take on rival third-seeded MidAmerica Nazarene Pioneers on Thursday, Feb. 28 at 8 p.m. in the first round of the HAAC conference tournament.
With the loss, BC falls to 18-11 and 10-8 in the HAAC and finishes in fifth-place in the standings.
Benedictine will take on fourth-seeded Central Methodist Thursday at 8 p.m. in Fayette, Mo.
The Wildcats struggled to score early in the contest and went scoreless for nearly five minutes after Todd Eils' game opening bucket.
Baker's next lead after Eils basket came at the 7:49 mark when EJ Carter put Baker up, 16-14.
Benedictine then went on a run with buckets from Shawn Fleming Jr. and Jonathan Anaekwe to go up 25-21 at the half.
Baker then went down by as many as nine points, 32-23, before clawing its way back to tie it up eventually at 40-40 with a free throw by Julian Mills.
The Wildcats first lead of the half finally came with 47 seconds left in the game when Honore hit a corner three to put the Wildcat faithful to its feet.
Baker then held on to win and send fellow seniors Samer Jassar, Baba Diallo and Kevin Lysaught onto senior night with a win.