Despite a superb Tom Pett strike moments before the interval for Boro, Ian Evatt's side emerged victorious in a hard-fought League Two clash, after two first half goals put them firmly in the driving seat.
Alex Revell made six changes from the side that played Northampton on Tuesday.
Scott Cuthbert, Ross Marshall, Ben Coker, Arthur Read, Charlie Carter, Tom Pett and Aramide Oteh all came into the side for the match.
However, Eoin Doyle's 15th minute shot put Bolton 1-0 ahead after Jamie Cumming saved well from Antoni Sarcevic, before Ali Crawford slotted past the on loan Chelsea keeper to make it 2-0 eight minutes before the break.
Despite Pett's outstanding effort - after Oteh's cross saw the Boro midfielder fire home from 18 yards - the home side could not make spells of second half pressure tell as Evatt's side went back to the north west with three valuable points.
Stevenage drop into the bottom two with eight points, three behind Scunthorpe, who sit in 22nd place.
Boro face a big week when they host Port Vale at the Lamex on Tuesday evening, before League One leaders Hull City visit on Sunday for the second round of the FA Cup.
Man of match:
Bolton's resolute defence deserved plaudits for keeping out a spirited Stevenage side, with goalscorer Pett excelling throughout. As did Boro's on loan Chelsea keeper Cumming as the visitors piled on the pressure.
Eoin Doyle impressed when grabbing the opener but Ali Crawford narrowly edges man of the match as Ian Evatt's men grabbed a welcome triumph to boost their bid to climb the table.
Alex Revell faces a big week:
Boro's beleaguered boss Revell is a dignified guy, and a former Stevenage player who knows the club inside out. He's faced an uphill task from day one this season.
After all he faced the start of the season not knowing which league his side would be playing in, thanks to the uncertainty around Macclesfield's appeal. And while not many League Two clubs have much money to throw around, Boro's budget is one of the lowest in the division.
Yet, Revell has never moaned about his plight and has simply got on with the task.
With Port Vale heading to the Lamex on Tuesday evening followed by League One leaders Hull City for their FA Cup second round clash that will be televised by the BBC on Sunday, Boro's former striker knows he has to grab a vital win from somewhere.