The TDS-entered ORECA-Gibson 07 entered under the Tower Motorsports banner suffered heavy damage when Thomas clouted the TF Sport-run D'Station Aston Martin Vantage GTE that Casper Stevenson had spun into the barriers at the fast sweeper before Tertre Rouge.
Several cars avoided the stranded machine before bronze driver Thomas, who was a late replacement for the original entrant John Farano following the Canadian's IMSA SportsCar Championship crash at Laguna Seca, locked up and hit British rookie Stevenson.
The stewards found that Thomas had failed to slow sufficiently before the impact, and will have to serve his penalty within four laps of it being formally announced by the race director when the 24 Hours gets underway.
TDS and D'Station both missed qualifying on Wednesday afternoon while replacement chassis were sourced, so will start from the back of the grid.
TDS driver Rene Rast told Autosport: "We're going to lose probably one and a half laps within the first 10 minutes, so that's very difficult to obviously catch up. I don't know what's possible.
"There might be a safety car, we might get the chance to get the lap back, but only if the race director decides to pull a safety car."
Source: Autosport