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."

The Class 700 Desiro City fleet is intended to ease overcrowding on the north-south route from Bedford to Brighton through central London.
Initial testing will be carried out at Three Bridges depot, then on the Brighton line before the train carries the first passengers next spring.
Thameslink said the new trains would transform the service for passengers.
The Class 700 trains will each have 12 carriages, instead of eight on many of the existing Thameslink services.
An extra 1,000 rush hour seats are promised between Brighton and London and 80% more peak seats across between Blackfriars and St Pancras in central London.
"The doors can open far more widely and people can get on and off the train more quickly, which means it can depart punctually," said Ruth Humphrey, project manager for Siemens which is building the trains in Germany.
All the new trains will be in use by 2018.
As well as the current Thameslink network and the Wimbledon Loop, they will be deployed across new routes from 2017 as part of Â£6.5bn Thameslink improvements currently under way.
Meanwhile, Chancellor George Osborne has said he is committed to a full study into building a second main line from Brighton to London (BML2).
The government has already said it will provide Â£100,000 for a new study into the reopening of the Lewes to Uckfield line in East Sussex.
In a letter to Conservative MP for Lewes Maria Caufield, Mr Osborne said he had extended the Lewes to Uckfield study, which would now also look at improving links between London and the south coast, including a feasibility study on BML2.

Of the 12 seats that were up for election, the Conservatives gained one with Matt Lacey taking the ward of Claines from the Liberal Democrats.
It means the Conservatives have 17 seats, Labour has 16 with the Lib Dems and the Greens holding one each.
Wyre Forest District Council also remains under no overall control and Labour retained control in Redditch.
It has 17 of the 29 seats in Redditch, after gaining two.
Conservatives remain the largest single party in Wyre Forest, with 15 seats, while UKIP were the big winners on the day, gaining five seats.
In Worcester, the council was controlled by the Conservatives until May 2013, with the support of two Lib Dem councillors.
Then the Lib Dems switched their allegiance, along with one Green councillor, to hand control to Labour.
Adrian Gregson, Labour councillor and current council leader, said: "There will obviously have to be some discussions on what happens next, with all the parties.
"We've held all our seats and have increased our votes in some of those, but the people of Worcester have said it's a really tight vote here and in most places have rejected the main national parties."
Conservative Simon Geraghty said: "I think it is time to have a discussion and see if we can do things slightly differently in Worcester."
Byron Harrison scored twice on his return to Stevenage, securing their first home win since November.
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The first of 115 new trains for the Thameslink network has arrived in West Sussex to begin tests.
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No party has managed to gain control of Worcester City Council following the local elections.