Cardinals general manager John Mozeliak said doctors have been trying to figure out the best way to treat Peralta since the middle of March. The medication Peralta was taking caused further illness to his stomach along with fatigue.
"They took some blood earlier in the week and realized some things were off balanced, and he had to get off the medication right away," Mozeliak said. "Subsequently, now he will be given some time to let that flush out and hopefully he will start feeling better.
"He knew something wasn't right but nobody really knew why. I still think there are some questions, but I think the good news is there is a strategy to try to get him back."
Peralta is off to a slow start, hitting just .120 without an extra-base hit or RBI in 27 plate appearances.
Jedd Gyorko and Greg Garcia will likely see the majority of the playing time at third base in Peralta's absence, which Mozeliak estimated to be anywhere from 10 days to two weeks. Cardinals manager Mike Matheny also said it is possible Matt Carpenter could see time at third base as well.
Lyons posted a 3.38 ERA in 48 innings over 30 relief appearances in 2016 before suffering a right knee stress reaction that caused him to go on the disabled list on July 31 and miss the remainder of the season. The left-hander underwent right knee surgery in November.
"He can serve a couple of different roles for us," Matheny said. "It will be nice to have him in the mix. He's a guy that can come in and face lefties and he can use his breaking stuff against right-handers, and being able to stretch him out is an option."
Lyons allowed just two runs over 14 innings in three rehab appearances for Triple-A Memphis.
"This is what you try to keep in the back of your mind, because there are a lot of days that weren't a lot of fun," Lyons said. "Your mind can play some tricks on you. This is the kind of stuff you think about to keep you going.
"I feel good. My body feels pretty good and my arm feels good. I'm just ready to pitch now."
With Lyons replacing Peralta on the roster, the Cardinals will move forward for the time being with 13 pitchers and just a four-player bench.
"In this next stretch, we'll see how things play out," Mozeliak said. "We've seen a good rotation, a not so good rotation and back to good. We'll let that play out for a little bit."
Andrew Gruman is a contributor to MLB.com based in Milwaukee. This story was not subject to the approval of Major League Baseball or its clubs.