Battling Barrow served up a scare for former boss Ian Evatt before bowing out of the Papa John’s Trophy with distinction.
Josh Kay and captain Niall Canavan scored the goals as Pete Wild’s side rallied from 2-0 down to level at two-all against hosts fifth in League One.
But the Cumbrians’ search for a famous victory over the one-time Premier League outfit ended in disappointment as substitute Elias Kachunga netted a 69th minute winner.
Even then the fourth-tier underdogs believed game-changer Dapo Afolayan handled in the area.
Instead, furious protests for a penalty were waved away and Evatt’s Wanderers moved to within three games of a Wembley final.
Barrow’s first ever run to the knockout stages of the ‘Pizza Trophy’ has netted the club £35,000 and further belief they can maintain their push for promotion from League Two.
Wanderers, winners of the 1989 edition of the competition, were the highest-placed team in the Northern section of the draw.
Also out of the FA Cup, the Trotters fielded a strong starting line-up and then brought on last season’s leading scorer, Afolayan, after 21 minutes due to Kyle Dempsey’s injury.
With his first touch, the ex-West Ham prospect stole in between Niall Canavan and Patrick Brough, punishing the duo’s hesitancy by heading in MJ Williams’ raking pass.
Harrison Neal’s block denied Afolayan a potential second as Wanderers looked to press home their advantage.
Patrick Brough got in the way of Kieran Sadlier’s drive while Paul Farman took the knee to save an effort from Dion Charles. Farman then tipped away Jack Iredale’s curling left foot effort.
In contrast, top scorer Josh Gordon was feeding off scraps against Wanderers’ 6ft 5in skipper, Ricardo Santos.
It was no surprise when Bolton doubled their lead seven minutes before the break.
Afolayan’s angled pass picked out Sadlier whose cross to the back post was slid in by Jon Dadi Bodvarsson.
So it was against the run of play when the visitors hit back after 42 minutes enabling Barrow’s nearly 600 fans to find their voice again.
Ex Holker Street favourite Joel Dixon spilled his first save of the game, failing to hold Ben Whitfield’s low shot.
Kay, once linked with a move to Bolton, fired in the loose ball as Afolayan complained in vain about a possible foul in the build-up.
Tom White replaced Neal at half-time as away followers taunted Dixon with chants of ‘you used to play for a big club’.
Whitfield tested Dixon from 20 yards and then his strong run and shot forced the corner from which Canavan levelled.
The resulting flag kick corner was flicked on at the near post and Canavan headed in unchallenged for his second goal of the season.
Barrow held parity until 21 minutes from time when another substitution again turned the contest Bolton’s way.
Afolayan’s shot was tipped onto an upright by Farman only for the rebound to drop invitingly for Kachunga whose tap in was only his third shot on target this season.
Barrow again rallied with Gordon’s goal-bound shot deflected for a corner. When the ball was delivered into the area Afolayan appeared to handle but referee Rebecca Welch was unimpressed.
And there was relief for the home side and disappointment for AFC at what might have been at the final whistle.
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