Abt stole victory right at the end when Edoardo Mortara spun out with Rosenqvist also overtaking the Swiss.
However, a post-race inspection revealed that the FIA security stickers on the inverters and motors did not correspond with those declared on one of his car's technical passport.
This breaches the series' technical and sporting regulations, and so Abt has been disqualified from the result.
Hong Kong ePrix
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Audi has one hour from the time of the decision - 6.55pm local time - to lodge an appeal.
Rosenqvist thus claims his second FE win, completing an unusual race for the Mahindra driver after he spun out of the lead at the first corner at the start of the race and recovered to second.
Abt's victory had launched him to the top of the championship after two races, but his exclusion means Saturday race winner Sam Bird now heads the table on 35 points, two points clear of Jean-Eric Vergne.
It has also gifted 2015/16 champion Sebastien Buemi 10th, meaning he at least has a solitary point to show for a dismal opening weekend.
Audi has also been fined €5000 for a separate infringement: five Audi team members walked onto the track to get to the podium before the final car had entered parc ferme, which the stewards deemed a "serious breach of safety regulations".
Abt's penalty is the latest high-profile exclusion for FE, and the third time the Abt-run FE has lost a win due to a post-race sanction.
Lucas di Grassi was stripped of wins in Berlin (in 2014/15) and Mexico City (2015/16), with the latter contributing to his title defeat that season.
Di Grassi then benefited last season when Renault e.dams driver Sebastien Buemi lost sixth- and fourth-place finishes in Berlin and Montreal.
Mortara inherits second place, while Mitch Evans is promoted to the podium - Jaguar's first in FE.
Earlier it had looked as if Mortara was easing to a commanding win when he lost the rear at Turn 2 on lap 43 of 45 and dropped to third, gifting Abt the win and promoting Felix Rosenqvist to second.
The race started under the safety car after a lights failure, and Mortara inherited the lead almost immediately when poleman Rosenqvist locked the rears and spun at the Turn 1 hairpin.

Race leader Rosenqvist spins out at Turn 1

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He dropped to 11th and as he started a gradual fight-back, Mortara edged away from Abt and established a decent lead in his Venturi.
Mortara's energy management was superior to his pursuers and he was more than three seconds clear after the mid-race car swaps, before Abt briefly cut that gap to less than two seconds.
With more energy at his disposal, Mortara responded with a sequence of personal bests and his lead had increased to more than three seconds again when he spun.

Mortara loses Hong Kong ePrix after dramatic late spin

He blamed a problem with the energy harvesting system initially, but later said it was a result of him pushing for fastest lap.
"I am gutted," he said. "I was struggling with the brakes at the end. It was my fault."
Abt swept past and made no mistakes as he secured his first win in FE - and first victory anywhere since the 2012 GP3 season - to give Audi a triumph in its first weekend as a full works team in FE.
Rosenqvist had a stunning recovery drive after his first-corner blunder, gradually rising through the order with a blend of aggressing overtaking and strong pace.
Mitch Evans looked like he might give Jaguar its first podium in FE after running third in the opening stint, but he then had a problem swapping cars and had to settle for fourth.
Alex Lynn was set to finish fifth for DS Virgin Racing but plummeted to 10th on the final lap as he ran out of energy, promoting Jean-Eric Vergne, Saturday winner Sam Bird, Oliver Turvey, Maro Engel and Nico Prost.
FE rookie Andre Lotterer ended a trying first weekend in the series with a heavy shunt at the final corner of the race - he speared into the barriers on the exit in bizarre fashion.
Abt's win launched him to the top of the points after the opening weekend's double-header, with Bird second after recovering from a 10-place grid penalty, but reigning champion Lucas di Grassi and 2015/16 title winner Sebastien Buemi still have zero points to their names.
Di Grassi suffered an on-track stoppage after the car swaps, but was running outside the points anyway, while Buemi made reasonable progress from starting last after his qualifying error but only made it back to 11th.
Hong Kong ePrix
Mortara loses Hong Kong ePrix after dramatic late spin
03/12/2017 AT 08:34