The injury, pending the result of scans, could potentially end Lyon's series, with Todd Murphy now set to play a major role through the rest of the series, having made his debt in the sub-continent against India just months ago.
The injury came while Lyon was fielding late on Day 2, with the 36-year-old in what was his 100th straight Test marking a remakrable run without major injury. He became the first specialist bowler in the history of the game to do so.
Lyon set off to take a catch on the fine leg boundary before pulling up lame.
"I haven't been up in the sheds yet, but obviously it didn't look good. It doesn't look ideal for the rest of the game," Steve Smith told reporters at stumps.
"I'm not sure how he actually is. But obviously if he's no good, it's a big loss for us.
"He's in his 100th consecutive Test match, which I know he was really looking forward to taking part in and having a role in as well. Fingers crossed he's OK, but it didn't look good."
If the injury is a tear to his calf, Lyon's Ashes are likely over, while a strain could see him return for the fourth and fifth Test.
The third Test is played on just a three-day turnaround, while the fourth Test is almost a full three weeks away from starting in Manchester on July 19.
Lyon had taken 1 for 35 from 13 overs in his first innings effort to date.