Orient had seen a 2-0 lead disappear as the battling Cobblers came storming back to level things up.
But, with the game drifting into stoppage time, Steele latched onto Donny Barnard's through ball and controlled it before beating a defender and firing past goalkeeper Lee Harper from 16 yards.
It was Steele's 16th league goal of the season - but it was rough justice on the visitors who had the better of the game and deserved at least a share of the spoils. However the goal propelled Orient to their first win in six games.
The home side had taken the lead against the run of play on 17 minutes when defender John Mackie slid in to touch home Daryl McMahon's excellent free-kick from the left.
The Cobblers continued to dominate the rest of the half, but all they had to show for their efforts before the break was a close range shot from Andy Kirk that O's goalkeeper Glenn Morris blocked with his legs.
Orient extended their advantage on 63 minutes when Steele latched onto a long goal kick from Morris and the striker coolly lobbed the ball over the advancing Harper.
But within five minutes Northampton's comeback was underway when Kirk, looking suspiciously offside, fired past the stranded Morris from eight yards.
Then, on 76 minutes, Martin Smith's free-kick was headed home by Town skipper Ashley Westwood.
After that it looked as if the visitors would go on and win the game, but it was Orient who finished strongly and two minutes from time Barnard set Steele free - but Harper made a wonder save touching his effort onto the bar.
But two minutes later an identical move cut Northampton open again and this time Steele finished in style to put a spoke in Town's promotion push.