League sources told ESPN and NFL Media that Thomas was benched after he had an altercation with a teammate during practice this weekend. According to the outlets, the altercation was with safety C.J. Gardner-Johnson.
Thomas had been listed as questionable with an ankle injury, but the Saints updated his status to out/not injury related on the team's final injury report Sunday.
The three-time Pro Bowl wideout has been sidelined by the ankle ailment since Week 1. He has practiced on a limited basis every day for two consecutive weeks.
In his only game this season, Thomas recorded three catches for 17 yards against the Tampa Bay Buccaneers.
Thomas led the NFL with 149 receptions and 1,725 receiving yards last season.
The Saints (2-2) host the Chargers (1-3) at 8:15 p.m. EST on Monday at the Mercedes-Benz Superdome.