This meant they gained an unfair advantage in collecting live data from other teams in pit lane, including tyre pressures.
Vandoorne did not progress from Group A Qualifying, finishing fifth 0.367s off the pace.
His team-mate Vergne did progress to the Quarter Final Duels although receiving the penalty and participating against Nissan's Norman Nato but was not quick enough to beat him, Nato's time of 1:09.118s seeing him progress.
“I don't know, it was a little bit difficult, the team told me just before Qualifying that I would start from pit lane because of an issue that happened for both Stoffel and I,” said Jean-Eric Vergne.
“I didn't want to know anything about it and to be honest, I'm a little upset, not because of that [the penalty] but because they told me before Qualifying.
“It changed nothing, it would have been better to know after Quali.”
Another championship contender who will start from the back of the gird is Mitch Evans, who was unable to get out for Qualifying after undergoing a new battery and gearbox after FP2 struggles.
The Portland E-Prix will then begin shortly after at 17:03 local time/10:03 AEST.