The Penguins (7-2, 4-1 Missouri Valley) trailed 17-7, but reeled off a 21-point run in the final quarter ignited by Hunter Wells' 58-yard strike to Andrew Williams. Webb's run capped a 3-play, 96-yard drive to surge into the lead with 11:15 remaining.
Youngstown State forced a punt, and Ruiz scored on a 2-yard run with 2:58 left.
Ruiz finished with 185 yards on 28 carries. Webb had 128 yards on 11 carries, including a 34-yard touchdown run to open the scoring in the second quarter.
Wells threw for 244 yards with an interception. Williams totaled 140 yards receiving.