The injury to the Ukrainian marred an otherwise satisfying night for the reigning champions with an eighth successive league win sending City back to the top of the table.
Zinchenko, who has been in superb form over the past few months, went down with a leg injury early in the first half and was replaced by Kyle Walker.
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And the boss admitted he feared he could be forced to miss some games.
“(It) Doesn’t look good. Right now I do not know but it is not looking good for the next games,” Guardiola said afterwards.
“We’ll see tomorrow. Fabian Delph is out - we don’t have many options.
“He (Zinchenko) is important for us. He knows the way we want to play but it is what it is.
“It happens during the season and he plays a lot of minutes, but we will find a solution. Danilo fought a lot in that position, but it is not his natural one. We will find a solution.”
“Phil played excellent. He did everything, arriving in the right positions with the right tempo. He always has chances, has a sense of goal. He's ready, we know it, to play any game in any position,” said Guardiola.
“He’s part of the group. This season he trains every day and in the locker room and he feels part of the group. I am glad the young age the way he plays.
“Every game he plays so far is good levels. The reception and the vision, he is an exceptional player. It’s not easy for him but he's patient and we delighted he's here, next season he will play even more minutes than he did this season.
“He’s calm and in the next decade he will be an important player for us.”
Reflecting on what was an eighth league win in a row, Guardiola added: “We played really well. We started really well with the goal from Kevin. Unfortunately we missed a lot of chances, we need to score more goals."