The two Toro Rosso drivers qualified near the rear of the field after grid penalties, and reverted to an older spec engine ahead of Saturday.
Both drivers lasted just four laps in the race before the pair spun out and returned to the garage in retirement.
Toro Rosso team principal Franz Tost says the incident was related to a piston as the brakes reached hot temperatures.
“It was a frustrating Sunday for Toro Rosso as both cars had to retire,” said Tost. “For whatever reason we ended up with very hot front brakes and one piston in the calipers got stuck.
“This caused the overheating of the brake fluid and a long pedal. Therefore, we called the drivers to come to the garage.
“Obviously, being in parc ferme conditions, we didn’t change anything from yesterday, so we need to investigate further what the reason is.”
Gasly took to Twitter after the race to reveal that his spin through the sweeping Turn 4 occurred at 280kph (174mph).
“Since the start of the race I had a really strange feeling with the brake pedal, it went pretty long and got worse very quickly,” he said.
“Then, on the third lap at Turn 4, I braked and the pedal went completely flat, so we lost all the front brakes and had to retire the car.
“We need to have a look at the data to see exactly what happened, but it’s just a shame to see both cars retire so early in the race.”
His teammate Hartley suffered an identical incident on the same lap, having overtaken Gasly earlier in the race before making an early stop as part of a strategy gamble requiring a lengthy second stint.
Hartley said: “I had a good start and passed Pierre before Turn 5, I was attacking the McLaren when the brake pedal went long.
“I reported it on the radio and then made our planned pitstop.
“We were going to try and be a bit cheeky with the strategy and do almost a full race on the softs, we had great tyre life and pace and think it would have worked.
“However, once I left the pits the pedal went completely to the floor, the rears locked and the car spun.”
Hartley added he was “excited” for Honda’s home race at Suzuka after the new engine specification produced what Tost described as a “big improvement” in performance in Friday’s practice sessions.