The dreary game looked set to be heading for a dull bore draw until substitute Kyel Reid - another newcomer - swung in a cross.
It was headed out by Jason De Vos, but McCann was hovering on the edge of the box to smash the shot home from 18 yards.
It was an impressive start for caretaker boss Simon Davey following the midweek sacking of Andy Ritchie.
Ritchie's controversial axing came after the newly-promoted Championship outfit were left floundering second from bottom of the table after only two wins in 15 league matches.
But it was grim fare for the 10,000 Oakwell faithful who had been baffled by the shock departure of this season's star performer Michael McIndoe to Wolves after signing from Doncaster Rovers just four months earlier.
The home side - with Academy manager Davey in charge - were poor, and with three new recruits making their debut, struggled to find any rhythm or creative flair, but Jim Magilton's mid-table Ipswich side were little better.
Barnsley's best first-half chance came courtesy of a 30th minute mix-up involving Ipswich keeper Lewis Price and defender Alex Bruce but Paul Hayes headed Leon Knight's cross wide.
Ipswich's leading scorer Alan Lee was inches short of heading in a Gary Roberts cross early on and Simon Walton lashed a wild volley over from another Roberts delivery.
De Vos headed wide early in the second half and, when Ipswich substitute Gavin Williams had a late opportunity with a dipping shot, Nick Colgan finger-tipped his effort over the top.
And as the home side continued to look for an opening McCann, on loan from Cheltenham Town, went close with a stinging shot.
At the other end Lee squeezed in another effort but Colgan produced a smart stop to deny the striker his ninth goal of the season.
Magilton switched strikers bringing off Jon Macken for youngster Danny Haynes, leaving Macken furious as he stormed into the dug-out.
But then in the dying seconds Barnsley grabbed the dramatic winner.