Three solid days of team scores kept the Pilots in contention for most of the tournament until the back nine of the final round which led to the third place finish behind winner Marian and runner-up Indiana Wesleyan.
Bethel started Monday's 36 hole, rain filled extravaganza with a solid team score of 300.
Junior Tim Langolf was the first round leader, firing a one over par 72 to bolster BC's attack.
The Pilots played well again in the afternoon and battled through the thunderstorms to shoot a 304.
Junior Brady Klotz, who had to finish his round on Tuesday morning after a long rain delay ended day one, carded an impressive 71 to lead the way for BC.
The Pilots shot 298 in the final round, with Klotz shooting a one-under par 70 and Freshman Drew Day adding a 73.
Jon Enfield, playing in his final collegiate tournament added 76, while Langolf and Brian Ulrich each shot 79.
Klotz, who fired 75-71-70 finished second overall in the tournament for the second straight year, missing out on a trip to the NAIA National Championship by a single stroke.
"It was tough going out there on a long day one and I was very proud of the way we competed," said Coach Chris Hess. "We were very consistent throughout and kept ourselves alive in the chase for this tournament all the way to the end. Jon Enfield had an amazing career at BC and it has been such a pleasure to coach a young man of such strong character and integrity. Brady made another great run at a trip to Nationals and he will join a strong group of returners next year."