Wanderers exited the Checkatrade Trophy after falling to a 1-0 defeat against Cheltenham Town on Tuesday evening.
The game itself passed without much action of note until the 90th minute when the home side were awarded a penalty kick.
Ben Alnwick was deemed to have upended Amari Morgan-Smith in the area, with the Town man stepping up to slot home from 12 yards to book the Robins’ place in the last 32 of the competition.
Wanderers made six changes from the side who started against Grimsby Town at the weekend with Ben Alnwick, Lewis Buxton, Dean Moxey, Josh Vela, Keshi Anderson and James Henry all in from the off.
Bolton started brightly in the clash with Henry’s wicked cross into the six yard box narrowly eluding an advancing Keshi Anderson.
The home side meanwhile enjoyed a chance of their own with Daniel Parslow seeing a long ball downfield bounce off David Wheater, but the Cheltenham man couldn’t get the direction needed on his effort to trouble Alnwick.
They proceeded to also see a Jordan Cranston long range effort deflect away for a corner kick, with a consequent effort from the set-piece being cleared off the line by Chris Taylor.
The latter then almost scored up the other end of the pitch when connecting with Lawrie Wilson’s cross, but his tame header was smothered by Town keeper Calum Kitscha.
It was a fairly contested clash inside the opening half of the first period, with neither goalkeeper being troubled too much.
Jamie Proctor looked certain to score on the half hour mark with a cross-cum-shot, but a last ditch challenge on the line denied him his second goal of the season.
The Robins were also looking dangerous on the counter though, with Billy Waters proving himself a menace as he pick-pocketed Liam Trotter on the edge of the box, only to fail to capitalise.
On the stroke of half time, Chris Taylor seemed to have broken the deadlock with a thunderous effort from long range, but his shot was cleared off the line as the first period ended goalless.
With no changes at the break, proceedings got back underway at a sodden Whaddon Road.
And the Whites nearly snatched the lead in the 51st minute, only for Anderson’s header at the back post from a Henry cross falling kindly for Kitscha.
The rain was still falling steadily at the LCI Rail Stadium, with the home side coming close through James Dayton at the near post with Alnwick doing well to keep his effort out.
Up the other end meanwhile, Proctor saw his shot from the edge of the box deflect narrowly over the crossbar with a goal seemingly imminent.
As the game progressed, so did Wanderers’ confidence on the ball with the hosts finding themselves penned into their own penalty area as Phil Parkinson’s men pushed forward in search of a goal.
Crosses aplenty were falling for the Bolton frontline, but with the torrid conditions were causing problems in terms of footing and composure at the crucial moments.
With just over ten minutes remaining meanwhile, the manager made a signal of intent as Wanderers had a triple substitution of Sammy Ameobi, Zach Clough and Max Clayton.
It was all out attack for both teams at this point, with Trotter’s strike from 20 yards being comfortably saved by Town’s keeper with six minutes remaining.
The lottery of penalties was looming, and with just a couple of minutes to go of the 90, it was all hands to the pump.
On the stroke of full time however, Cheltenham were handed the opportunity to take the lead from the penalty spot after Alnwick upended Amari Morgan-Smith, with the Town man brushing himself down to slot home the resulting effort from 12 yards and earn Town's progression in the competition.