The defender came off shortly before half-time for Niall McGinn, who earned the Dons a point with a well-placed free-kick.
McInnes believes that Vyner, on loan from Bristol City, may need surgery after a re-occurrence of a previous knock.
"There's a concern there. Last time (he was injured) he was out for three weeks," he said.
"The specialist said he didn't need an operation. There will be a revisit to the specialist and between ourselves and Bristol City we'll make the decision that is best for Zak.
"I think there's a real risk that he might need the operation that was suggested prior, which would mean he would be out for the season."
If surgery was needed, McInnes revealed that the Dons would be prepared to recruit in January.
"We're already without Greg Leigh for two months, Craig Bryson goes in for his operation in the next couple of days," he added.
"If that (surgery) is the case we can do smart work in January and bring two or three additions in."