The Trotters were without Kieran Lee, who was self-isolating, and made a number of changes with Harry Brockbank, Arthur Gnahoua, Lloyd Isgrove and Ben Jackson all dropping out of the starting eleven.
Ian Evatt's side had won just one of their last eight, but would be looking to change their fortunes against a Stevenage side who were battling relegation.
Bolton Wanderers: Gilks; Jones, Almeida Santos, Baptiste, John, Delfouneso, Thomason, Williams, Maddison, Afolayan, Doyle.
Stevenage: Stockdale; Luther-Wildin, Prosser, Vancooten, Coker, List, Lines, Pett, Aitchinson, Newton, Norris.
Story of the match
The attacking pressure prevailed for the Boro, as Lines and Jack Aitchison both squandered opportunities to find the breakthrough.
But despite it being against the run of play, it was the home side who snatched the lead courtesy of Declan John. Oldapo Afolayan, making his first start for the Trotters, laid the ball back to the left-back who rifled the ball past David Stockdale to propel Bolton in charge.
The opener nearly sparked a second for the Bolton, as Marcus Maddison's cross was nodded into the side netting by last season's League Two top scorer, Eoin Doyle.
However, Lines continued to concern the Bolton defence, as he slid an intelligent ball through to Aitchison but his low strike was thwarted by the legs of Matt Gilks.
This hectic first half continued, as Maddison and Doyle linked up nicely in the Stevenage box before the ball fell loose to Trotters defender Alex Baptiste, but his strike was dealt with.
Heading into the break, Bolton had one final opportunity to double their advantage but Stockdale was present to contain Ricardo Almeida Santos' headed effort.
Into the second half half and Almeida Santos had a similar chance, but could only head over from six yards out to spare the blushes of some poor Stevenage marking.
Stevenage continued to hunt an equaliser, but Norris' volleyed strike fell narrowly wide of Gilks' goal.
However, Bolton's defending of their lead was made considerably harder in the 78th minute, as Williams, making just his second appearance, was dismissed by the referee for a shocking late challenge on Tom Pett, denouncing the Trotters to ten men.
The Boro looked to immediately capitalise, as Remeao Hutton's long throw was nudged towards goal by Norris, but Gethin Jones was present to clear what was almost an equaliser.
But as Matty Stevens and Lines both came close to spawning a late fightback, it was the valiant defending of Bolton that proved the victor as the home side completed the double over their League Two counter-parts.
A performance that Evatt should be pleased with, as Bolton proved courageous in snatching three points in what was a defensively pleasing Wanderers performance. The defence, Gilks included, all put their bodies on the line for the badge today, keeping out some dangerous attacking prospects in the form of Norris and Aitchison, and even rallied together following the sending of Williams.
Stevenage will be rightly frustrated, as the Boro came close to stealing a point from the University of Bolton stadium but instead leave Lancashire empty handed. Lines in midfield has an excellent outing, controlling the tempo of the game. Whilst Alex Revell may be frustrated, the performance was promising against a Bolton side who were very much financially aided.
Trotters left-back Declan John proved today that he is more than capable of performing at the level he once did back at Cardiff City and Rangers, scoring an impressive goal and defending excellently in the Bolton back-line.