"Everybody is fine," Indians manager Terry Francona said.
Hitters had the choice of whether or not to swing, and pitchers had the option of using an L-screen. Shortstop Asdrubal Cabrera sent a chopper back at Masterson, who was struck on a heel. Second baseman Jason Kipnis swung at a pitch from Pestano and hit the reliever on the side of his left shin.
Pestano, who had a noticeable bruise after the workout, said he was fine.
"I threw a hanging two-seamer to a left-handed hitter," Pestano said. "That's what they do to it. That sent me a message: Don't do that again."
Francona said throwing from behind a screen is often awkward for pitchers.
"They get more out of it throwing without that L-screen," Francona said. "I think they're all more comfortable doing it, and the drill is all for the pitchers. The hitters, for the very most part, just track balls. A couple guys swing, but they know going in this is still the pitchers' time to get ready in their progression. I thought everything went pretty well."
Besides Masterson and Pestano, other pitchers who threw in Tuesday's live sessions included Ubaldo Jimenez, Carlos Carrasco, Scott Kazmir, Bryan Shaw, Cody Allen, Nick Hagadone, Joe Martinez, Giovanni Soto, Matt Langwell, Jerry Gil, Preston Guilmet and Trevor Bauer.
Cleveland will resume live batting practice Wednesday, though the mound sessions will be moved to the indoor cage if it rains as forecasted. In that scenario, hitters will stand in but will be instructed not to swing.
Jordan Bastian is a reporter for MLB.com. Read his blog, Major League Bastian, and follow him on Twitter @MLBastian. This story was not subject to the approval of Major League Baseball or its clubs.