Lewis-Moore was carted off the field, and afterward Ravens coach John Harbaugh called it "a major injury."
"Early indications are that it's his (left) Achilles," Harbaugh said. "I was really disappointed for a guy who had the ACL last year. It's going to be tough for him and we'll rally around him. He'll be back stronger than ever next year."
Lewis-Moore missed 2013 after suffering a torn right ACL at the end of his college career at Notre Dame. Baltimore picked him in the sixth round of the 2013 draft, and he was making progress in camp this summer.
The Ravens already lost another defensive end, rookie Brent Urban, earlier in camp with a torn ACL.
"To lose those two guys with all that potential, and they've been doing so well in camp is unfortunate," linebacker Terrell Suggs said.
Baltimore cornerback Asa Jackson was also hurt Sunday. He was helped off the field with what Harbaugh termed "a minor ankle thing" that would keep him out for "some number of days. We'll see. But it's not a major deal."
Jackson also had been playing well in camp while competing for a starting cornerback spot. The Ravens are growing thinner at corner since starter Lardarius Webb is already is out with a back injury.
Two San Francisco players were injured in the practice — guard Adam Snyder and wide receiver Quinton Patton. Offensive coordinator Greg Roman said that it's too early to say about the injuries of either player.
In spite of the injuries, both teams seemed happy with the joint practices, which began Saturday and run through Monday.
The teams lined up at one point for a goal-line drill with live hitting and tackling — but run with just the backups.
"The whole thing is a great test and a great learning experience for us," San Francisco defensive coordinator Vic Fangio said. "I've done over 20 of these joint practices in my days, and they're always very good and very beneficial."
San Francisco tight end Vernon Davis was one of the 49ers who especially enjoyed the trip because he's from Washington and played his college football at Maryland.
He also didn't participate in the team's offseason work because of concerns with his contract, but showed up for training camp and this trip to Baltimore.
"It feels good to be back with the guys," he said. "It brings back a lot of memories playing in College Park, and it's definitely been great being back here and seeing some of the family and some of the guys I went to school with."