The loss saw Derek Adams’ team dropped one place in the table from second to third.
For the second time within a week, Argyle found themselves two goals down, but unlike against AFC Wimbledon on Tuesday night in the Johnstone’s Paint Trophy, the Pilgrims could not pull it back against Teddy Sheringham’s Stevenage.
The home side took the lead in the sixth minute through on-loan Spurs midfielder Connor Ogilvie.
Argyle had plenty of possession after that but could not score and in the 38th minute Stevenage doubled their advantage when Chris Whelpdale tapped in a ball across the line by Charlie Lee.
Substitute Craig Tanner got Argyle back into the game with a goal in the 54th minute.
The visitors turned up the heat after that but Stevenage dug deep. Argyle thought they had equalised 20 minutes from time when Carl McHugh had the ball in the net, but it was disallowed by referee Gary Sutton.