Toure landed heavily after challenging for a first-half header and immediately crumpled to the ground.
It was instantly obvious the Ivorian would not be able to continue, leaving manager Roberto Mancini to hope the damage is not too extensive.
Toure's departure marked the low point of a generally disappointing night for the Blues, which was salvaged by late goals from John Guidetti and Shaun Wright-Phillips, who lashed home the winner six minutes from time.
With the Carlos Tevez affair rumbling on, the picture seemingly getting more confused rather than less, City could have done with a convincing performance, just to reassure their fans everything else was proceeding as planned.
They were not helped by an awful pitch, which needed to pass an afternoon pitch inspection for the game to go ahead, such has been the rain that has lashed the Pacific coast over recent days.
Unfortunately, City were unable to produce the performance Mancini would have wished.
Adam Johnson was lively but City's best player was Joe Hart, which just about summed it up.
Hart denied Eric Hassli and Camilo Sanvezzo with excellent saves before he was eventually beaten in rather fortuitous circumstances for Vancouver as Alexandre Morfaw's shot deflected in off Stefan Savic.
Sanvezzo then had another goalbound shot saved by Hart before curling a free-kick into the side-netting which the City keeper appeared to have given up as a goal.
A pre-season friendly is never a time to panic. It is four weeks' tonight before City open a Premier League campaign that promises so much against Swansea after all.
The concern will be Toure's injury.
Goalscoring hero of the FA Cup final and semi-final, the giant Ivorian is a big part of Mancini's side in more ways than one.
To see how much pain he was in after landing awkwardly following a routine aerial challenge did not bode well and he had to be assisted in making his way very slowly to the visitors' dressing room.
Mario Balotelli was amongst those introduced at the break, although it was the hosts who should have added a second when Long Tan stabbed wide after being left on his own at the near post, barely three yards out.
Guidetti eventually restored parity with a far-post header midway though the second-half, although by then Balotelli was committing some niggly and unnecessary fouls, and it was left to Wright-Phillips to score the winner late on.