Stevenage extended their unbeaten run to four matches at the expense of Bury.
Byron Harrison fired the visitors in front after the ball broke to him in the box.
Mark Roberts extended Boro's lead when he beat the Shakers offside trap and headed past keeper Cameron Belford from Joel Byrom's cross.
The hosts got back into the contest when Lenell John-Lewis was fouled by Lawrie Wilson in the area, and Andy Bishop converted from the spot.
VIEWS FROM THE DRESSING ROOM
Bury manager Richie Barker told BBC Radio Manchester:
"Obviously it's a disappointing result, and to a certain extent a disappointing performance as well.
"I thought we wasted the first 45 minutes. Our tempo was too slow, we didn't move the ball quick enough and didn't work the goalkeeper.
"I thought we kept the ball really well but there is no point in keeping it in the middle third as you won't get anywhere."
Stevenage manager Graham Westley told BBC Three Counties Radio:
"It was disappointing to concede the goal, it would have been our fourth clean sheet on the bounce. We were disappointed to see the penalty awarded.
"We deserved to be two up, and certainly as the game wore on there was only going to be one side that was going to score again. If it had got to three, four or five, I don't think anyone could have complained.
"We knew we had progressed more than they have, and we came here today to prove that point and it was a nice victory to get."