He was replaced by Nathan Peterman, who led the Bills on a go-ahead touchdown drive before throwing an interception that was returned by Houston for the game-winning score with less than two minutes remaining. Peterman was intercepted again on Buffalo's ensuing possession.
Peterman chalked up his pick-six, returned 28 yards by Texans cornerback Johnathan Joseph, to being "just a bad decision" on a short pass toward the sideline intended for wide receiver Kelvin Benjamin.
"It's something I'm going to learn from," Peterman said. "Critical time. I just thought there was so many lessons for me to learn and get better from."
Peterman has appeared in seven games, including the AFC wild-card playoff loss last season, since he was selected in the fifth round of the 2017 draft. He has thrown 10 interceptions in those games, including five in the first half of his starting debut in November, and two before he was benched for Allen in last month's regular-season opener.
"We got to have more respect for the football," coach Sean McDermott said of Peterman's two interceptions Sunday. "I thought he tried to force the football in those situations. You can't do that. You have to take what the defense gives you."
Peterman completed six of 12 passes for 61 yards, including a 16-yard touchdown pass to wide receiver Zay Jones early in the fourth quarter.
Allen, the No. 7 overall pick in April's draft, was hit in his right elbow by Texans linebacker Whitney Mercilus after releasing a pass on what became a 39-yard completion to Benjamin.
Allen shook his right hand as he ran to the huddle after the completion, remaining in the game to throw an incompletion on the next play. Allen then took a knee and was walked to the sideline by trainers. He remained on the bench but did not re-enter the contest.
Allen did not speak to reporters after the game. McDermott said Allen's injury was being evaluated.
Peterman was active as the Bills' backup quarterback Sunday over veteran Derek Anderson, whom the team signed last week.