It was a cup tie which had a bit of everything.
Five goals, woeful defending, a stirring late fight-back and both managers sent to the stands after a confrontation.
Wednesday deservedly trailed by three goals after strikes by Dorian Dervitte, Adam Armstrong (pen) and Jem Karacan.
But Bolton withstood a late onslaught, with Jordan Rhodes grabbing a brace to set up a grandstand finish.
Injuries deprived Carlos Carvalhal of the services of Glenn Loovens, Sam Hutchinson and Kieran Lee. New signing Frederico Venancio didn’t have international clearance.
Carvalhal wouldn’t take risks with his senior stars and rotated his squad. Only Tom Lees, Daniel Pudil, Adam Reach and Barry Bannan retained their places. Yet he still fielded an attack-minded side. Rhodes, Sam Winnall and Fernando Forestieri all returned.
Forestieri, making his first start since his training ground scuffle with Winnall, was stationed on the left hand side of midfield. It is not a position he feels comfortable but he put in a hard-working shift.
Wednesday made the early running and Reach’s rasping left foot strike deflected over the crossbar after good approach play. Forestieri then dragged an effort wide of Ben Alnwick’s right hand upright.
Bolton, without a league win since sealing promotion back to the Championship, could have gone ahead in the ninth minute when Mark Little floated in a teasing delivery but Aaron Wilbraham glanced wide.
Trotters captain Karacan and Pudil were yellow carded after rash, late tackles in a scrappy opening 45 minutes.
Rhodes wasted a glorious chance to end his goal drought, sending a free header over the top from Ross Wallace’s corner.
It was then Winnall’s turn to fluff his lines. After failing to test Alnwick with a header, the former Barnsley man prodded Reach’s centre off target.
Wednesday lacked a cutting edge and their poor finishing cost them dearly.
After surviving a big let off in the 38th minute when Derik Osede steered Will Buckley’s corner wide, the Owls failed to heed that warning and Dervitte rifled an unstoppable volley past Joe Wildsmith.
Wednesday only had themselves to blame for not going into the break all square as Forestieri somehow had a shot hacked off the line. A goalmouth scramble then ensued before Wallace lashed over.
A lovely pass by Forestieri released Bannan but the in-form midfielder’s delicate chip was easily saved by Alnwick as Carvalhal’s men finished the half on top.
The Owls poured forward in numbers after the re-start, leaving gaps at the back which Bolton duly exploited.
It took an inch perfect tackle by Bannan to deny former Wednesday loanee Buckley a sight at goal after a run by Adam Armstrong.
But Bolton kept piling on the pressure and the lively Armstrong slipped in Buckley, who was brought down by Wildsmith. Referee David Webb showed no hesitation in pointing to the spot. Armstrong coolly sent Wildsmith the wrong way.
Forestieri almost conjured a goal out of nothing. He superbly turned his marker in the penalty area before shooting wide. And Karacan compounded the Owls’ misery in the 64th minute, looping a wonderful header over Wildsmith after a peach of a cross by Antonee Robinson.
Bolton took their foot off the pedal and Wednesday threw everything at them.
Rhodes ended his 17 match goal drought in the 76th minute, keeping his cool in the six yard area to send a shot underneath Alnwick. After Rhodes reduced the deficit, subs Atdhe Nuhiu and Marco Matias were both thwarted.
It was one way traffic and Rhodes expertly headed in Matias’ cross to set up a thrilling finale.
Matias and Bannan tried their luck to no avail. And tempers boiled over after a mistimed tackle by Bannan. Bolton boss Phil Parkinson and Carvalhal clashed, both being sent to the stands.
Defeat halted the Owls’ fourth-match unbeaten run. Promotion to the Premier League is Wednesday’s top objective this season but it was a missed opportunity to maintain momentum. Their defending left a lot to be desired and a late rally shouldn’t disguise a disjointed display.
Wanderers: Alnwick; Darby, Dervite, Beevers; Little, Karacan (Pratley 69), Derik, Buckley (Morais 65), Robinson; Armstrong (Le Fondre 73), Wilbraham. Substitutes: Subs: Howard, Taylor, Madine, Earing.
Owls: Wildsmith; Palmer, Lees, Pudil, Reach; Wallace (Joao 74), Bannan, Abdi; Forestieri (Matias 70); Winnall (Nuhiu 69), Rhodes. Substitutes: Dawson, Hunt, Jones, Fox.
Attendance: 6,385, (2,602)
Star man: Barry Bannan