The hosts led when Harrison ran onto a long goal kick that had bounced over Cambridge keeper Josh Coulson, and tapped the ball into the net.
Ben Williamson hit the post for Cambridge as they looked to level.
Stevenage sealed the win when Connor Ogilvie's drilled cross found Harrison, who converted from close range.
Harrison helped Stevenage secure promotion to League One in 2011, and is back at the club on loan from Chesterfield.
Stevenage caretaker manager Darren Sarll told BBC Three Counties Radio:
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"It was a good performance. We've come away from that knowing that that's still not our best. There's still so much to do in terms of improving us.
"There's real signs of the old Stevenage coming back. Standing shoulder to shoulder, and we won't be beat. I love that mentality, that's the mentality that I've been brought up on here.
"I thought we could have done better in the first half. To be a little more authoritative with our football, to go after Cambridge a little bit more than we did. There's lots to be pleased with, more so the fact we can beat sides above us."
Byron Harrison scored twice on his return to Stevenage, securing their first home win since November.