Shenandoah (22-6-1, 16-4 ODAC) was a 3-2 winner in the opener before Lynchburg (14-20, 9-10) came back to win 8-6 in the nightcap.
SU had locked up the No. 1 seed at next week's ODAC Tournament following the completion of play on Wednesday, but LC needed at least one win today to keep its tournament hopes alive.
Lynchburg will now play at Washington and Lee Sunday morning in a must win game in order to qualify for the six-team ODAC Tourney.
As the No. 1 seed, Shenandoah will play the first game of the tournament Thursday morning against the No. 6 seed (either Eastern Mennonite or Lynchburg).
Joe Coleman had singled to short with one out, sending Arens up against LC starter Brandon Miller (2-6).
Arens doubled into the right field corner, sending Coleman all the way around from first with the winning run.
Shenandoah scored two runs in the second inning of game two and matched LC's two runs in the fourth, but could not answer Lynchburg's four run seventh combined with two more in the eighth.
Nolan Overby cut the deficit in half with a two-run HR in the ninth before Lynchburg completed the upset victory by turning its second double play in as many innings.
Shenandoah completes its regular season on Sunday with a 1 p.m. non-league doubleheader against Marymount.