Brown (4-3, 1-3) led 17-14 after Cody Taulbee ran one in from 1 yard out with 3:37 left to play.
However, Dexter Davis returned the ensuing kickoff 46 yards and Ragone completed two passes for 15 yards, then ran for another 6 to set up Loftus' game-tying field goal.
Ragone finished with 165 passing yards and 46 rushing yards.
The Bears took over with 2:12 remaining but Trevor Neimann picked off Patrick Donnelly's third pass of the possession, giving the Quakers (3-4, 3-1) the ball on the Brown 44.
Ragone then ran for 17 yards on two carries and completed a 2-yard pass to Eric Fiore to set up Loftus' game-winning 35-yard field goal.
Donnelly completed 30 of 47 passes but threw four interceptions.