The Owls’ had substitute Leon Knight to thank for their point. A 72nd minute replacement for Shefki Kuqi he thumped home a low drive from the edge of the area to punish Gills, down to ten men following the 80th minute dismissal of player-manager Andy Hessenthaler.
The Preistfield chief was sent off for two bookable offences and could only watch as his side conceded the late leveller and even came close to losing.
Gerald Sibon and Lloyd Owusu both had chances to earn Wednesday their first ever league win in Kent.
Hessenthaler will now face a one-match ban and will miss out on playing against Stoke City, now managed by Tony Pullis the man who signed him, in a fortnight’s time.
Gillingham, who had lost their two previous home games against Wolves and Reading, had to work hard before taking a 24th minute lead through Tommy Johnson.
Richard Hill said "To concede so late makes it seem like a defeat. People will point to Andy Hessenthaler’s sending off as the moment that cost us the game. He came in afterwards and said sorry but you can’t do anything abut it now.
“I thought the all round game was solid and Sheffield made it hard for us.