The Belgian had come on as a second-half substitute and been instrumental in turning the game in City's favour.
He scored the goal that put them 2-1 ahead on the night and crossed brilliantly for Sergio Aguero to head home and give City a 4-3 aggregate victory.
De Bruyne suffered a painful end, however, when his knee appeared to give way in the 89th minute and he was carried off with his leg in a brace.
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"I'm optimistic he won't be out for the rest of the season," City manager Manuel Pellegrini told the BBC.
"We'll see how important the damage is. It's not the cruciate ligament."
Pellegrini said the club's doctor thought it was a problem with De Bruyne's medial ligament.
"Kevin has been a very important player all season," he said. "Tomorrow we will have news but it is not a nice injury."
The injury could have a significant impact for both club and country, with City still fighting on four fronts and Belgium having qualified for this year's European Championship in France.
City are second in the Premier League table, three points behind leaders Leicester City, and play Dynamo Kiev in the Champions League last 16.
They travel to Premier League rivals Aston Villa in the FA Cup fourth round on Saturday.
(Reporting by Toby Davis; editing by Ed Osmond/Greg Stutchbury)
