Clemens was in his third inning of work after relieving starter Brett Oberholtzer and was facing Lowrie for the second time, with Oakland leading, 8-1, in the seventh.
"Just a fastball inside," Clemens said. "[Catcher Carlos Corporan] set up in, we wanted a fastball in. I didn't get behind it and I cut it."
The pitch plunked Lowrie in the backside. Despite some command problems during his outing, the hit-by-pitch seemed more than a coincidence after last week's flare-up in Oakland.
In that instance, the A's shortstop attempted a bunt to beat Houston's shift in the first inning of a game Oakland already led 7-0.
Clemens threw several pitches that landed near Lowrie's legs, and Houston manager Bo Porter even had some choice words for Lowrie after the inning before returning to the dugout and angrily shoving a cooler.
Porter was surprised that Clemens was tossed without a warning from the home-plate umpire and also denied the apparent bad blood between the teams.
"I don't see it as frustrating, I don't see it as something to get past," Porter said. "What are we getting past?
"You'd have to ask them that [if they see it as intentional]. I can't answer for somebody else."
Lowrie was more than willing to share his opinion on the incident.
"It's flat-out embarrassing," Lowrie said. "There's no other way to say it. Every perspective, every angle you look at it, it's embarrassing. That kind of conduct should be condemned.
"I still don't understand why it was made into a big deal to begin with. And then he throws at me twice in Oakland, and then throws at me again today. For a number of reasons it's embarrassing, but that in particular ... and, I had him in an at-bat before, I hit a double off him, and then he throws at me the first pitch. I've never seen anything like it. It shouldn't be condoned."
Lowrie said he had no doubt of Clemens' intent.
"It's pretty obvious that he was throwing at me on purpose for the third time," Lowrie said. "I thought it ended in Oakland. I said this then. If they want to continue to hold a grudge, that's up to them. Clearly they've taken it very personally."
"There was no carryover on my end," Clemens said. "What happened in Oakland was squashed in Oakland. Bad pitch there, and it just so happened I cut a fastball. The guy's been hot, swinging a good bat ... we wanted to let him know I'm not afraid to come inside. That happens sometimes. So be it."
Porter said all the right things, but ended his final answer regarding Clemens' intent quite cryptically.
"I think the game of baseball takes care of itself," the manager said. "George Springer got hit tonight, too. It's part of the game."
Another dismal outing against the A's and Clemens on the mound was a recipe for some fireworks. The righty again provided them, this time earning him an early shower and potentially some disciplinary action from Major League Baseball.
That would be bad news for an already-depleted Houston bullpen, as Matt Albers is dealing with a sore right shoulder and closer Josh Fields sat out Thursday's game after three straight days of work.
Chris Abshire is a contributor to MLB.com.
This story was not subject to the approval of Major League Baseball or its clubs.