Perry Ng and Yousef Salech netted as the Bluebirds left Greater Manchester with all three points on Saturday afternoon.
Brian Barry-Murphy made a single change to the team that defeated Premier League Burnley in midweek, with Gabriel Osho coming into the starting XI in place of Will Fish. Fish was joined on the substitutes bench by fellow central defender, Dylan Lawlor, who returned from injury.
From the start of the game, Barry-Murphy's side were in the ascendency. Perry Ng saw a low effort blocked after seven minutes, while Ryan Wintle's 25-yard powerful strike was tipped away by Wigan Athletic goalkeeper Sam Tickle seven minutes later.
It was full-back Ng who gave City the lead 17 minutes in. Perry linked up well with Rubin Colwill, and his strike across goal took a deflection which beat Tickle in front of the 2,300 Bluebirds supporters behind the goal.
City will have been slightly disappointed not to add to their lead considering their dominance in the fixture, with Calum Chambers and Rubin also seeing efforts go off target.
The Bluebirds were almost punished by their hosts late in the half, as the Latics created two chances. The first of which saw returning forward Christian Saydee test himself against Nathan Trott one-on-one, but the City shot stopper come out on top, with a fine save. On loan Wrexham man Paul Mullin also had an opportunity moments later, but he couldn't get his header on target.
City's right-back was proving the danger man in this one, with Ng going close to a second goal on the hour mark. Our No.38 struck at goal left footed from the edge of the box, but Tickle made a fine stop in the Wigan Athletic goal.
The home side knew that while the deficit was just one, they could find a way back into the game and saw two efforts go close with 70 minutes on the clock. Captain Jason Kerr headed over, with substitute Dara Costelloe seeing his header saved from Trott moments later.
Anything but a victory would have been tough to take for Brian's Bluebirds. Thankfully, that second goal to seal the win did come eventually, deep into added on time as substitute Yousef Salech was fouled as he looked to reach Rubin Colwill's through ball.
Latics defender Morgan Fox was shown a red card for hauling down the City striker, before Salech took on the responsibility himself, sending Tickle the wrong way to secure three important points on the road.
Next up for City are three home games on the bounce, starting at CCS on Tuesday evening against Burton Albion - 7:45pm kick-off.
FINAL SCORE: WIGAN ATHLETIC 0-2 CARDIFF CITY
Wigan Athletic: Tickle, Fox, Aimson (McManaman 83'), Murray, Wright (Cooper 65'), Saydee (Raphael 83'), Mullin (Costelloe 65'), Trevitt (Adeeko 55'), Kerr, Smith, Hungbo. Subs Not Used: Savin, Sessegnon.
Cardiff City: Trott, Ng, Chambers (Lawlor 74'), Osho, Bagan, Wintle, J.Colwill (Turnbull 74'), R.Colwill, Ashford, Davies (Willock 64'), Robinson (Salech 64'). Subs Not Used: Turner, Fish, Kellyman.