Fowler's knee buckled during an 11-on-11 drill. He dropped to the ground, grabbed his leg as he rolled from side to side, and eventually got helped off the field. He was able to put some weight on the leg and was later carted to the locker room for tests.
Jaguars coach Gus Bradley said the team is still evaluating Fowler and will know more about his status Friday night.
"I didn't really see what happened on the field. It happened kind of off to my side," Bradley said. "But we'll find out more tonight."
Offensive tackle Watts Dantzler, who was engaged with Fowler when the DE went down, said he didn't know what happened to cause the injury.
"I really honestly have no idea," Dantzler said. "I was just kicking, got a punch on his shoulder, and he just went down. I don't really know exactly what happened. I feel terrible about it."
When Dantzler went to the sideline afterward to apologize, he said Fowler replied, "You're good, man. It's just football."
Bradley said some of the rookies, who hadn't played since January, appeared tired. The coach said the team was adjusting the practice to manage rust and nerves.
"I think you've got to be smart," he said. "You weigh it to, 'Hey, we can get them acclimated, a feel for everything.' But we didn't have a regular practice as far as reps. Where we normally go 15 reps, we had 10."
The Jaguars are counting on Fowler to be a centerpiece of the defense. They expect him to be a Day 1 starter, meaning he will replace 33-year-old veteran Chris Clemons.
Now they are waiting for more information on the player they selected with the No. 3 pick in the draft April 30.
"Sometimes injuries happen in the game," Bradley said. "It's just hard for me to speculate what took place and things like that. Anytime a guy gets injured, it's not a pleasant thing, it's not a good thing, whatever the injury is, because it can set him back a week or couple days or whatever. Whatever it is, we'll deal with it and keep going."
The Associated Press contributed to this report.