The Falcons (2-3, 0-1 Mid-American Conference) had taken a 21-17 lead on Tyler Sheehan's 8-yard run with 5:11 left.
Jones' catch from Schmitt capped a six-play, 77-yard drive that took just 45 seconds.
Jones led the Hurons (2-4, 1-2) with 60 yards on 13 carries and also had four catches for 61 yards. Dwayne Priest ran for a 12-yard score and Terrence Blevins added another TD on a 1-yard plunge for Eastern, which had 410 yards of total offense. Schmitt completed 21-of-29 passes for 253 yards.