The Astros placed the veteran reliever on the 15-day disabled list and recalled Jon Singleton from Triple-A Fresno on Friday. Singleton, who was not with the club for batting practice, arrived in time for the game, a 3-2 loss to the Yankees.
Qualls heads to the disabled list with a pinched nerve in his neck, an injury he said he's had for a while but decided to bring to the attention of the training staff on Thursday.
"It's been over time. I'm hurting myself and hurting the team by going out there so I finally decided to speak up," Qualls said. "Can't really keep trying to throw through it, it's the best course of action.
"I'm not a big guy to make excuses for myself out there, but I think we need to get it taken care of so I can be 100 percent."
In Qualls' last four appearances dating back to his June 17 outing against Colorado, he's allowed four hits, two earned runs and a home run to the 12 batters he's faced. He took the loss vs. the Angels on Monday, dropping his record to 1-4.
Astros manager A.J. Hinch said he didn't notice anything off during those last few outings, but he said the move to the DL was the wise thing for the club in the long run. He added Qualls was set to get an MRI at some point Friday.
Singleton is the Pacific Coast League leader in home runs (17), RBIs (66) and runs (56). At the time of his callup, he was hitting .280 with a .387 on-base percentage and a .553 slugging percentage.
"I'm definitely in a better place," Singleton said. "I understand my swing more, so to speak, than I did in Spring Training. Everyday is a work in progress and I'm trying to get better."
Singleton hit .168 in 95 games with Houston last season, including 13 homers and 44 RBIs. Hinch said the reports he's gotten about Singleton were all positive, and he thinks Singleton can have a better second stint at the big league level, just as some of his teammates have done.
"We've seen the growth of Domingo Santana, and through my years I've seen guys that their second or third time around they feel better," Hinch said. "They know their routines, they know what to expect, a little more comfortable playing in a big stadium."
Singleton's arrival also creates a logjam in the Houston lineup. Chris Carter is entrenched at first base and Evan Gattis at designated hitter -- both spots where Singleton primarily plays.
"It creates what we talked about in Spring Training -- three guys for two spots," Hinch said. "It's something I'll have to navigate through every day and communicate with the players and figure out how the best lineup could be. If there's too many good choices, that's fine. I understand there's going to be someone on the bench that's unhappy, but so be it.
"You earn your keep around here, perform well and make it hard on me. That's what I'm going to tell all three of them."