Town mounted a comeback over the final half an hour but despite George Thomson reducing the arrears they came away empty handed
After a busy opening to the season, manager opted to freshen things up with James Belshaw, Dan Jones, Connor Kirby and new signing Calvin Miller coming into the side. Joe Cracknell, Warren Burrell, Lloyd Kerry and
Brendan Kiernan all dropping to the bench.
Bolton boss Ian Evatt also shook things up, making five changes from last week's 2-0 defeat at home to Newport in a bid to check a start to the season saw them without a point or goal from their opening three league games.
Town had the brighter of the opening minutes and with a spate of pressure penning Wanderers in their own area Aaron Martin met Josh Falkingham's cross, but saw his effort denied by the foot of the post.
And almost immediately Town found themselves a goal down. Nathan Delfouneso attempt at goal was thwarted by the home defence but from the resulting corner an unmarked Eoin Doyle struck first past time past a helpless Belshaw.
Doyle almost doubled his tally just minutes later with only a smart clearance from Jones preventing Town falling further behind.
The goal rattled Town, with the changed line-up struggling to find their groove aside from the occasional moment. New-boy Miller saw his sharp left-footed shot test Crellin in the Bolton goal and a half shout for a penalty involving Falkingham failing to entertain referee Speedie.
Town came out with more purpose after the break but although Martin got himself on the end of Falkingham's cross minutes into the second half he couldn't keep his shot on target.
Martin's afternoon was done shortly after as Weaver made his first change with the striker being replaced by Kiernan.
Barely a minute later though Town fell further behind as Doyle this time turned provider, playing in Delfouneso to increase the visitors lead.
The two-goal deficit wouldn't last for long though as Town hit back just four minutes later with Thomson coolly slotting home from Miller's cut back.
As Town pressed for an equaliser they were reminded of the threat Bolton posed when Sarcevic shot from
distance to force a smart save out of Belshaw in the slippery conditions following a day of rain in South Yorkshire.
Weaver made his third and final change with fifteen minutes remaining with Jon Stead thrown into action. And he saw his side come close over the final stages when Ryan Fallowfield's ball flashed across the six-yard box to safety and Kiernan was narrowly adjudged offside when well set.
But ultimately, their final efforts were in vain as Wanderers held on to register their first victory of the season.
Town: Belshaw, Fallowfield, Jones, Smith, Hall, Thomson, Falkingham, Kirby, Miller (Walker,69), Beck (Stead, 75), Martin (Kiernan, 56)
Subs not used: Cracknell, Burrell, Kerry.
Booked: Jones (45), Falkingham (71)
Goal: Thomson (61)
Bolton: Crellin, Jones (Hickman, 42), Almeida Santos, Delaney, Delfouneso, Doyle, Sarcevic, Crawford, Mascoll (Gordon, 71), (Comley, 76), Brockbank.
Subs not used: Taft, White, Dacy, Gnahoua.
Booked: Gordon (73), Hickman (90)
Goals: Doyle (11), Delfouneso (57)
Referee: Benjamin Speedie.
Report by Danny Pugsley.