The Venturi driver had enjoyed a strong drive through the lower end of the points to claim fifth once the results were taken from the end of the 29th lap owing to the Turn 6 crashes for Nick Cassidy, Lucas di Grassi and Vandoorne that brought out a red flag.
But under a brief full course yellow ahead of the race stoppage, Mortara was found to have surpassed the maximum speeds required under FCY conditions and thus takes a five-second penalty.
This relegates the Swiss driver to ninth in the final classification, meaning he earns just three points from the opening race of the Brooklyn double-header.
Mortara's pain has been eased following similar penalties for Jake Dennis and Mitch Evans, which moves Dennis down from eighth to 10th - although Evans' final finishing position of 11th is unaffected.
The penalties lift Sebastien Buemi into fifth place, ahead of Pascal Wehrlein - who lost drive after an accident with Buemi moments before the red flag to cause a minor pile-up with Dennis and Sam Bird.
Bird has been promoted to seventh, while Nyck de Vries moves up to eighth.
In further penalties, Andre Lotterer has been handed a 10-second penalty for causing a collision with Antonio Felix da Costa, which yielded a puncture for the Portuguese driver that eventually proved to be terminal.
Oliver Askew has also been handed the equivalent of a drive-through penalty - converted to a 21-second addition to his total race time - for failing to use both activations of attack mode.
Buemi was investigated for the contact with Wehrlein but, due to the nature of the heavy rain impinging on the drivers' visibility, was cleared by the stewards.
Wehrlein was also cleared of any unnecessary stoppages under the full course yellow, following the incident with Buemi causing damage to his Porsche.
With five races remaining, Mortara has 142 points from Vandoorne's 137, while Jean-Eric Vergne sits third in the standings with 128 points. Evans remains in title contention with 124.
