A moment of magic from Mark Davies helped Wanderers register their first away points of the season at Hillsborough.
The midfielder struck superb left-footed effort midway through the second half to secure a 2-1 win in front of 2,400 travelling fans in South Yorkshire.
Moments earlier Ross Barkley had drawn Sheffield Wednesday back level from the penalty spot after Anthony Gardner had been tripped inside the box.
This all came about after Marcos Alonso had given Wanderers a half-time lead having headed in his first goal of the campaign two minutes before the interval.
Bolton were good value for the three points, with Chris Eagles once again enjoying another outstanding performance in a free role in midfield.
The win could have been by a bigger margin had more fortune fallen David Ngog’s way, with the French striker having two decent openings in the first half and another shortly after the break.
Ahead of kick-off, Owen Coyle recalled Keith Andrews to his team, making one change from the loss at Birmingham four days earlier. Chung-Yong Lee dropped down to the bench with Marvin Sordell not included in the matchday 18.
Having been Bolton’s star man in the opening month of the season, Eagles was once again causing problems from the off.
With just three minutes played, the winger felt he should have earned his team a penalty when he went to ground inside the box under a clumsy looking challenge from Martin Taylor. However, referee Keith Stroud was unmoved despite strong appeals from the dugout by boss Coyle.
Eagles also played his part in setting up Ngog, who shot straight at Kirkland from a tight angle, while the former Liverpool keeper did well to save from Mark Davies after the diminutive midfielder had ghosted in at the near post.
Sheffield Wednesday’s main threat was rapid winger Michail Antonio with the 22-year-old a constant outlet down the right flank for the Owls.
Twice he forced Bogdan into the action inside the opening 20 minutes, firstly with a long-range shot and secondly after outpacing Zat Knight and prodding goalwards from five yards out.
The closest Wednesday came to breaking the deadlock inside the first half was when Rhys McCabe clipped the outside of the post with a free-kick from 30 yards out.
The first period ended with Wanderers in the ascendency as Coyle’s charges conjured up three great opportunities to get themselves ahead in the quarter hour leading into the half-time break.
Eagles curled inches wide of the post having drifted into the area from the left and Ngog, twice, missed the target from close-range when unmarked. The Frenchman planted a free header wide before ballooning into the Spion Kop after being picked out by Mark Davies.
It was only a matter of time before Bolton went ahead, and they did just two minutes before half-time through the unlikely source of Alonso.
The Spaniard drifted in at the near post to glance a left-winged corner from Eagles into the net beyond the helpless Kirkland.
Bolton came out after the break and looked to build on their advantage and Ngog was literally inches away from doubling the lead in Wanderers’ first attack after the restart. After a great low cross through the six-yard box from Alonso, the former Liverpool man somehow managed to avoid making contact on the ball underneath the Wednesday crossbar.
Having not managed to net that important second goal, the hosts – backed by 25,000 vociferous fans - came roaring back into the game, levelling the scores on the hour mark from the penalty spot.
Andrews was adjudged to have tripped Anthony Gardner inside the box and after referee Stroud had pointed to the spot, Ross Barkley buried into the bottom corner from 12 yards.
The score was to stay at 1-1 for just three minutes as Mark Davies produced stunning goal to restore Bolton’s lead.
Picking up possession just outside the box, the midfielder waltzed past two attempted challenges before thrashing a left foot volley into the top corner of the goal. Kirkland, unmoved, just watched as the ball slapped against the back of the net.
Davies’ strike knocked the stuffing out of Dave Jones’ team, with Wanderers more or less controlling the remainder of the contest.
Barkley drilled narrowly wide and Nejc Pecnik sliced a volley over in the latter stages but a resilient second-half defensive showing ensured Wanderers moved into the top half of the Championship table, taking their points tally into double figures in the process.
Sheffield Wednesday: Kirkland, Jones, Gardner, Taylor, McCabe (Semedo 46), Barkley, Bothroyd (O’Grady 75), Rodri (Johnson 58), Antonio, Pecnik , Lee (Subs not used: Bywater, Llera, Beevers, Madine)
Wanderers: Bogdan, Mears, Mills, Knight, Alonso, Andrews (Pratley 90), Spearing, Eagles, Mark Davies, Ngog (Afobe 65), Kevin Davies (Subs not used: Lonergan, Petrov, Warnock, Ricketts, Chung-Yong)