Baker shot a three-round score of 945, 28 shots behind winner CMU. Baker shot a 312 in the first 18 holes, a 308 in the second and 325 on the final day.
They finished ahead of third-place Missouri Valley (954), third-place Avila (954), fifth-place Graceland (955) sixth-place Evangel (960) and seventh-place Culver-Stockton (987).
Andy Kelley finished in the Top 5 with a tie for fourth-place and defending HAAC Men's Golfer of the Week Alex Zuzelski took 10th.
Kelley shot an impressive 71 in the first 18 holes, which proved to be the lowest round of any golfer on the weekend. He then followed that up with a 76 and 80 for a total of 227.
Zuzelski shot an 80 and a par 72 on day one and finished his round with an 83 for a three-day total of 227.
Kelley Thompson finished the tourney with a 14th-place finish round of 239, Grant Grego took 20th with a three-day score of 244 and Mason Dick took 30th with a score of 260.
Baker ends its season with two first-place finishes, three second-place finishes and had four HAAC Men's Golfer of the Week winners, Thompson, Grego and Zuzelski (twice).