Keller was taken to a local hospital for further evaluation, and the Coyotes said they would update his status Thursday.
"We know it will be long term," Arizona coach Andre Tourigny said. "He'll recover. For now it's not the injury, it's the human. It's Kells the person. He competes so hard. Seeing him in pain and having a significant injury, that's extremely tough."
Keller was hurt with 5:15 remaining in the third period. He was skating toward the Sharks' net when he got knocked off stride and crashed into the boards behind the goal. He remained prone on the ice for about five minutes before being wheeled off, giving a thumbs-up sign as he left.
Jan Jenik scored twice, including the tiebreaker in a three-goal third period, to help the Coyotes snap a six-game losing streak.
"A lot of emotions out there," Jenik said. "Glad we were able to come out with a win, but obviously we lost our best player."
Keller, whose mother was in attendance, leads the Coyotes with 28 goals and 35 assists.
"I know that him and [Sharks defenseman Nicolas Meloche] made some contact, probably five seconds before that happened," San Jose coach Bob Boughner said. "It looked like he just lost an edge or lost his balance going in. He went in pretty nasty. Not good to see."
The Associated Press contributed to this report.