Verstappen effectively brought Q1 to an early end when he brought out the yellow flags following a sudden loss of power late in the session, but it was the manner in which he parked his stricken car that caught the attention of the stewards.
The Dutchman had at first pulled to the left, only to then turn right and cut across the track as he rolled to a stop. The stewards deemed that action as "potentially dangerous" and penalised the Toro Rosso driver accordingly.
"Car 33 experienced a sudden power loss at the exit of turn 11," read the stewards' statement. "The driver initially moved to the left side of the track towards a safe position and when it was about to stop, moved to the right onto the racing line, where it eventually stopped. This caused double yellow flags to be shown and endangered oncoming drivers."
Verstappen, who qualified in 15th, is therefore set to start Sunday's race at Suzuka from 18th.
"Certainly not the best of days! I had a sudden loss of power, all the electricity shut-down in the hairpin and from there on I couldn't do anything," he said of the incident. "It's very frustrating, because the car was going very well, but in the end it is what it is… We might be on the back foot again before the race, but we never give up."
Verstappen is not the only man facing a grid penalty: Force India's Nico Hulkenberg takes a three-place drop into Sunday's race due to his clash with Williams' Felipe Massa in Singapore, while Daniil Kvyat will be forced to start from the pit lane after his high-speed crash in Q3 necessitated a chassis change.
