The Whites headed into the break trailing by two goals to nil, however a close-range header from Neil Danns and a perfectly executed penalty from Andre Moritz deservedly put Bolton back level at the DW Stadium.
Having wrestled back the impetus, Bolton were dealt a cruel blow with 22 minutes remaining as McManaman’s deflected effort wrong-footed Andy Lonergan to seal the points and a 3-2 win for Uwe Rosler’s men.
Bolton boss Dougie Freedman made one change from last weekend’s 3-0 victory over Doncaster Rovers at the Reebok Stadium.
On-loan midfielder Danns, who scored the last goal of the game against Rovers, stepped in for winger Chris Eagles.
The notable inclusion for Wanderers however was Mark Davies, who was on the bench, following a long lay-off through injury.
It was a fiery atmosphere at the DW Stadium, with over 4,500 fans making the short trip from the Reebok to show their support for Dougie Freedman’s men.
In the ninth minute, the hosts were controversially awarded a penalty after Matt Mills was adjudged to have handled a McManaman cross. After some hesitation the decision was eventually made by the linesman.
Watson, a former team mate of Freedman at Crystal Palace, stepped up to rifle an unstoppable spot kick into the top right hand corner, sending Andy Lonergan the wrong way.
The contest continued to be played at a frantic pace, but in the 24th minute, Bolton’s task became even harder as the Latics extended their lead.
Showing fantastic technique, Wigan striker Nick Powell connected with a deflected cross to send a looping bicycle kick over Lonergan.
Powell looked to add a quick-fire third for the FA Cup holders minutes later but a strong right footed strike from the edge of the penalty box was comfortably collected by the Bolton custodian.
Bolton’s first chance to test former England international Scott Carson came on the half-hour mark and it was an opportunity made in Cardiff.
Loan pair Kevin McNaughton and Joe Mason, both on loan from the Bluebirds, linked up excellently on the right hand side, with the full-back picking out a run to the front post by Mason, who ghosted away from his marker, but the striker’s header was met by a strong hand from Carson.
Bolton continued to put the pressure on as they looked to halve the deficit before the interval, and only a late goal line clearance denied the Whites and Brazilian playmaker Andre Moritz.
The chance came courtesy of clever wing play from Chung-Yong Lee, who skipped away from an Emerson Boyce sliding tackle on the left. The South Korean international sent an inviting cross to the back post for Moritz, but his header was scrambled away by Leon Barnett.
One final opportunity fell the visitors’ way before Kevin Friend blew for half time, as centre half Mills looked to replicate Powell’s overhead kick exploits but the ball flashed wide of Carson’s left-hand post.
A rejuvenated Wanderers side came out for the second period and started in perfect fashion by clawing a goal back within three minutes of the restart.
An initial free-kick from Moritz from 25-yards was palmed away by Carson. However, Lee recollected the ball for Bolton to ensure the danger for Wigan wasn’t over. Possession eventually worked its way out to Moritz on the right flank and he dinked a cross into the box for Danns to head home.
Moritz went in search of his third goal in a Bolton Wanderers shirt just before the hour mark but his venomous strike from fully 30-yards was straight down the throat of the goalkeeper.
Again, the Whites went knocking on the Wigan door as Moritz and Danns linked up once more but this time the on-loan Leicester midfielder could only head skim the cross bar with Carson beaten.
In the 64th minute Moritz was rewarded for his efforts with his second goal in as many games.
The equaliser came from the penalty spot as referee Friend was given no option but to point to the spot after Boyce caught Lee in the face with a trailing late leg.
Stepping up positively, Moritz showed a cool head to slot the ball into the far right hand corner in front of the travelling support from BL6.
With the contest now on a knife’s edge, it was turning out to be a fantastic derby at the DW Stadium, with both teams pushing forward at every given opportunity in search of the all-important fifth goal.
And it was winger McManaman who dealt Bolton a cruel blow in the 68th minute and scored what would turn out to be the winning strike.
Unmarked on the edge of the penalty box, McManaman’s low effort took a heavy deflection off Danns which consequently diverted away from Lonergan to nestle in the far corner.
Despite the set-back, Bolton continued to pile bodies forward in search of another route back into the contest.
Manager Freedman made two attacking substitutions with ten minutes remaining, with Jermaine Beckford and Mark Davies both introduced for Danns and Darren Pratley respectively.
However, with Moritz, Beckford and Mason all coming within a whisker of giving the Whites parity, they were unable to turn the game around as Wigan claimed all three points.