His return was one of four changes made by the Irish manager Nigel Worthington, with Steven Davis, Kyle Lafferty and Gareth McAuley also recalled for the game in Maribor.
McCann was replaced after 73 minutes with the game scoreless, but goals from Milivoje Novakovic and Zlatan Ljubijankic gave the home side the win.
"We played some good football and showed a tremendous work ethic, but the rub of the green is not with us. We have got to make things happen," said Worthington.
"The players were very down in the dressing room, as you would expect, but I was very proud of their performance. We created some decent chances - and if we can start taking them, we will pick up points."
Northern Ireland have just two points from their three games in Group 3, they play San Marino on Wednesday.