Keating had put the sole Chevrolet Corvette C8.R on pole by 1.5 seconds during the Hyperpole session on Thursday.
The car he shares with Nicky Catsburg and Nico Varrone is among the favourites to take the class spoils - and it currently leads the GTE Am World Endurance Championship standings.
However, in the night-time session following the Hyperpole contest, Keating was deemed by stewards to have failed to slow sufficiently and was handed a stop/go penalty, which was served during the final minutes of the session.
The penalty therefore doesn't affect Corvette's hopes of ending its eight-year win drought at Le Mans in the final year of the GTE division featuring at La Sarthe.
It was not Keating's only penalty of the session as he was also fined for speeding in the pitlane.
Prior to qualifying, Keating had spoken of how he was trying to repeat his success in the class last year, when he won as part of TF Sport's Aston Martin line-up.
"It would be incredible to win at Le Mans and hear the American national anthem as an American driver," he said, adding "it would be incredible to win Le Mans in a car that I sell in the dealership in Texas".
Keating was not the only driver to be penalised for failing to slow down, and a five-minute stop/go was also handed out to the #66 JMW Motorsport Ferrari after Giacomo Petrobelli was ruled to have not respected a slow zone during the same FP4 session.
The 488 that Petrobelli shares with Thomas Neubauer and Louis Prette is due to start 19th in the GTE Am class.
A car that does have a penalty hanging over it for the race is the #13 TDS-entered ORECA-Gibson 07 LMP2 machine after it was given a three-minute stop/go after Steven Thomas failed to slow sufficiently in the opening practice session on Wednesday, when Casper Stevenson's D'station Aston Martin was stranded in the middle of the track after spinning just before Tertre Rouge, and Thomas ploughed into the stricken car.
An earlier version of this story incorrectly stated the penalty would need to be served during the race - we apologise for this error
