The speedy rookie fell awkwardly onto his glove hand while trying to stop a ball up the middle hit by David Ortiz from reaching the outfield before getting up and committing an error on the throw home as Shane Victorino came around to score.
However, manager Bo Porter said the rookie had actually injured the thumb when he was caught stealing at third base during the fourth inning.
"He did it on a slide into third base, so it was sore when we went out to talk to him [in the sixth]," Porter said. "We took him out to try to get the soreness under control and treat it. It was already bothering him at that point."
Porter had not yet met with trainers regarding Villar's status before speaking to the media following the loss.
Villar said after the game that the injury "isn't serious" and moved the thumb normally -- he was noticeabl favoring it -- to try and prove it.
"Listen to the trainers and maybe come back and take some batting in the cage tomorrow," Villar said of the plan going forward. "Take some ground balls and test it and see if [I] can put pressure on it."
Villar was 2-for-2 with an RBI and a run scored before his departure. He also stole a base but was caught stealing on his other attempt. He now has 10 steals in 15 games.
Jake Elmore replaced Villar at short, the first time anyone else has played the position since the Dominican Republic native was called up July 22. Elmore was an adequate substitution at the plate, lacing a solo homer in the eighth inning.
Villar's exit coincided with the Astros' demise in the game, as Houston surrendered five runs in the sixth inning after already squandering 5-0 and 7-3 leads.
Chris Abshire is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.