Freeman pounced at the death after Jo N’Guessan’s equaliser had completed a busy start to the second half that had seen Walsall take a 2-1 lead through Malvind Benning and Craig Westcarr.
Jimmy Smith had got Stevenage up and running in the first half prior to the three goals to begin the second with Freeman’s winner giving Boro their first win since March 8.
It took Stevenage 35 minutes to break the deadlock as Smith found himself unmarked and fired home from close range, leaving Saddlers goalkeeper Richard O’Donnell rooted.
Three goals in the opening eight minutes of the second half followed as Milan Lalkovic found Benning, who equalised before Romaine Sawyers’ long-range effort was saved by Chris Day.
Walsall did go in front though moments later as Westcarr tapped home although the lead did not last long with N’Guessan being played through by Smith and calmly sliding home.
And already-relegated Stevenage completed a remarkable comeback in the 82nd minute as Freeman tapped home from close range as pressure built on Walsall.