Scottish midfielder McCabe, a summer signing from Rangers, slammed home a superb volley from the edge of the penalty area midway through the first half and Frenchman Helan marked his final game for the Owls before his return to parent club Manchester City with the second in the fourth minute of time added on.
Charlton, who lost their first league game in eight at Bolton last week, turned in a disappointing display and mustered only two efforts on goal throughout the match.
Wednesday midfielder David Prutton had already forced a fine save from Charlton goalkeeper Ben Hamer with a 20-yard volley and team-mate Anthony Gardner twice went close with stinging shots from the subsequent corner before McCabe broke the deadlock in the 20th minute.
Owls defender Miguel Llera's inswinging corner was cleared by Charlton's Lawrie Wilson but only as far as McCabe, who was lurking on the edge of the penalty area and arrowed a sweetly-struck volley into the top corner.
The home side then threatened to run riot as winger Michail Antonio fired in
an angled drive that was well saved by Hamer and then lashed another effort from outside the penalty area just wide.
Antonio was proving a real menace to the visitors and he rifled another shot just off target in the 32nd minute, while striker Chris O'Grady's effort from inside the area was caught by Hamer.
Charlton enjoyed an equal share of possession during the first half, but failed to muster a single effort on goal.
Chances at either end after the break were few and far between, with only Gardner's 56th-minute header threatening Hamer, who then held on to O'Grady's angled drive, while Wednesday goalkeeper Chris Kirkland remained completely redundant.
The Addicks, who had failed to score in two of their last three matches, had still not had a single shot by the hour-mark and boss Chris Powell withdrew Salim Kerkar in the 63rd minute and sent on fellow striker Ricardo Fuller, returning to action after a four-game lay-off due to a hamstring injury.
Wednesday were dealt a blow when Prutton was forced off injured and replaced by Chris Lines in the 67th minute.
Fuller had the visitors' first shot two minutes later, but his 25-yard effort was blocked by Llera and with 12 minutes left Powell sent on forward Rob Hulse and midfielder Danny Green for Danny Haynes and Emmanuel Frimpong respectively.
But it was Wednesday who threatened again. Helan, pushed up into midfield in his last match for the Owls, fired a shot straight at Hamer from the edge of the box and although another Fuller effort was blocked by Owls defender Lewis Buxton, Helan made the game safe for the Owls by stabbing home from close range in the fourth minute of injury time.