The Crusaders won game one, 2-1, then picked up the sweep with a 6-3 win over the Wildcats.
With the loss, Baker fell to 6-29 and 3-15 in the HAAC, while Evangel improved to 28-13 and 13-5 in the conference.
In game one, Brett Lechien got the start and threw all seven innings. He allowed just two earned runs and six hits.
He also went 1-for-3 from the plate with an RBI. Baker managed just four hits with Josh Zach leading the way with a 2-for-3 game.
All three runs came in the third inning, with Evangel scoring two in the top half and Lechien knocked in Charles Coleman for Baker's one run.
In game two, both team's offenses stepped up, as Evangel had 12 hits and Baker had nine. Zach had two more hits and Justin Lane went 2-for-4.
The Wildcats scored first in the bottom of the second inning, as Bryan Kindle led off the inning with a double to right field, then Lane came up and singled to centerfield and scored Kindle.
Baker then was shutout until the eighth inning. Baker trailed 5-1 in the bottom of the eighth and cut the deficit to two, 5-3 with a two-run four hit inning.
Ethan Jacks led off the inning with a single and then Lechien singled to right field scoring Jacks. After a Zach single, Josh Ackerman then singled to right field scoring Matt Fry.
Three pitchers saw action for Baker with Ryan Hahn getting the start. He threw four innings, giving up four earned runs and one hit.
Then Derek Schupp came in to pitch three innings and Tevin Thompson threw the final two innings.
Baker will next take on Peru State for a four-game set this weekend, as they take on the Bobcats on Saturday and Sunday at 1 and 3 p.m.