The substitute had only been on the pitch 12 minutes when he smashed home the right footed strike to give Swindon all three points.
Barnet midfielder Nick Bailey had put his side ahead after 18 minutes with a left footed strike after Michael Pook lost the ball in the Swindon defence.
Ricky Shakes equalised on 53 minutes with an intended cross that went over the goalkeeper and into the top left hand corner.
Swindon got off to a bright start and after two minutes Shakes headed over from a cross when he really should have scored.
Barely a minute later Christian Roberts crossed to give Shakes a free header but the midfielder headed over again.
Swindon completed a hat-trick of near misses when Monkhouse put his right footed shot past the right hand post when he had a clear shot on target.
Dennis Wise made tactical change at half time taking off Pook and putting Paul Evans into centre midfield.
The change worked as Swindon came out of the blocks with renewed fight and vigour. There was constant pressure on the Barnet goal, but Swindon could not break down their defence. Roberts went close on 56 minutes when he lobbed the keeper but the ball went past the left hand post.
Barnet midfielder Dean Sinclair almost took the game away from Swindon when his header was narrowly off target from Liam Hatch's cross.
Swindon continued to press in the last 10 minutes as Barnet struggled to get out of their own half.
The constant pressure looked to be getting no rewards until Brownlie's injury time winner.
Roberts almost added a third with a right footed strike, but Lee Harrison in the Barnet goal tipped it round for a corner.