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."
Both teams are hopeful of getting their cars ready by the end of third practice on Thursday, with Stevenson needing to complete 10 laps in darkness to be allowed to start the race in the car he shares with Satoshi Hoshino and Tomonobu Fujii.
Explaining the crash, Stevenson told Autosport that he'd been pushing "a bit over the limit" on cold tyres when he "got a tank slapper on".
"I saved it once, saved it twice and then it just fired me into the wall. I think that would have been two or three hours' worth of repairs.
"Then I was collected by the LMP2, which has completely destroyed the car.
"I'm not so angry with him - I understand from a driver's point of view. I put myself in the middle of the track, so it's a mistake from my point.
"If we can have a good race now, it would be a good comeback story."
TF Sport boss Tom Ferrier told Autosport: "It completely did the shell the second hit. The chassis is gone, so we ended up bringing our ELMS car over, which arrived at 9am this morning.
"We'll take the gearbox from their car in that. There was an option to try to reshell right from the start but it's such a big job, you've got to put brake lines in and wiring, so this is easier.
"It's the chassis that we had at home and had all the electronics and brakes in it. If we can fix it and get it to the end, it will be a happy car crew."
