Hoyer, who also suffered a strained neck and is dealing with a wrist injury, is doubtful for Sunday's game against the Indianapolis Colts, the coach said.
"He took a beating last night," O'Brien said. "I think they were checking him out for all the various injuries."
Hoyer was evaluated for a concussion during the fourth quarter of the 27-6 loss, less than a month after his previous concussion diagnosis. He was sacked five times by the Patriots and frequently attended to by the Texans' medical staff on the sideline. Overall, the Texans gave up six sacks, the most they have allowed all season.
Backup quarterback T.J. Yates took the Patriots' sixth sack.
Hoyer came into the game having been diagnosed with a concussion four times while playing football, including once in high school, once in college and once during his rookie year in the NFL.
Most recently, he suffered a concussion against the Cincinnati Bengals on Nov. 16. In that game, he suffered memory loss and couldn't remember the plays.
"Whenever you suffer a concussion like that, multiple concussions within a five- or six-week span, obviously the player himself is concerned about that, and nobody's more concerned than I am because of my relationship with Brian and his family," O'Brien said. "I think that the Houston Texans will always do what's best for the player."
After Hoyer's departure from the game, the Yates-led Texans went on to beat the Bengals and then the New York Jets in the following game, which Hoyer missed.
O'Brien expressed confidence in Yates' ability to replace Hoyer if he can't play.
"I think we have a good guy there to step in because he's a pro and he's got really good poise," O'Brien said. "He's a bright guy. I told the team that today. I told the offense that too."
Hoyer completed 11 of 22 passes for 155 yards with no touchdowns and no interceptions against the Patriots. He completed only four passes in the second half. The Texans were limited to seven first downs in the loss.
Heading into the game, Hoyer had 18 touchdowns in nine games. He had thrown multiple touchdown passes in seven games, including five starts.
ESPN's Adam Caplan and Tania Ganguli contributed to this report.