The Eagles (3-5, 2-3 Pioneer) closed to 47-42 on Jake Raymond's 5-yard run with 3:13 left. On the winning six-play, 58-yard drive, quarterback Austin Gahafer threw 22 yards to Bornhauser with the latter then completing an 18-yarder to Gahafer. Three plays later, Bornhauser scored for the second time Saturday.
Valparaiso led 24-14 at halftime before the teams combined for 37 points in the third quarter.
Gahafer passed for 352 yards - including a career-high 116 for Raymond - with three touchdowns and an interception.
Brandon Hall had 120 yards rushing for Valparaiso, which scored on punt and kickoff returns.
The teams totaled 962 yards offense.
The win was Morehead State's eighth straight over the Crusaders (2-6, 0-4). A minimum of 52 points has been scored in the last five meetings.