Whincup had held off arch rival Scott McLaughlin through two pitstop cycles – the cars pitting together on both occasions.
McLaughlin eventually found a way through at Turn 2 with 17 laps to go, taking the win and a one-point lead over Whincup in the championship.
That gap has now blown out to 76 points, with Whincup fourth in the standings behind McLaughlin, David Reynolds and Shane van Gisbergen.
Stewards confirmed the penalty this evening, noting that data from all cars was checked as part of a review by Sporting & Technical Director, David Stuart.
"Following a report from Supercars Pit Lane Officials, it was alleged that Car #1 deactivated the Pit Lane Speed Limiter prior to the end of Pit Lane following a pit stop," read the stewards' bulletin.
"A report from the S&TD included a detailed review of the Supercars Telemetry Data and Control ECU Data for Car #1 which confirmed that Car #1 did not have its Pit Lane Speed Limiter activated at all times whilst it was moving in Pit Lane in breach of Rule C15.4.2.
"Additionally, compliance with Rule C15.4.2 was checked for all Cars in Race 9. No other breaches of Rule C15.4.2 were established.
"The Competitor, Triple Eight Race Engineering, admitted the breach and the Stewards imposed a post- Race Pit Lane Penalty (38 seconds) to be added to Car #1’s Race Time for Race 9."
Speaking in the post-race press conference before the penalty was handed down, Whincup said he'd feared a penalty may have been coming for speeding at pit entry on his first stop, due to a hit from behind by McLaughlin.
Further down the order, Simona De Silvestro was handed a 15-second penalty for contact with Jack Le Brocq at Turn 10 on lap four.
The sanction demoted the Nissan driver from 23rd to 24th, behind James Golding, who served an in-race penalty of 15 seconds for turning De Silvestro around at Turn 10 four laps later.
Of the De Silvestro/Le Brocq incident, the stewards’ summary read: “Following the Race, at the request of Nissan Motorsport the DRD conducted an investigation into an allegation that Car #19, Jack Le Brocq, had brake-checked Car #78, Simona de Silvestro, at Turn 10 on Lap 4,” the stewards’ summary read.
“After reviewing judicial camera footage of the Incident from Car #78, the DRD determined that Car #19 had not committed any breach of the Rules, but Car #78 had driven carelessly in breach of Article 2.1.1 of the Code of Driving Conduct (Schedule B2) in causing contact with Car #19 causing Car #19 to spin and lose positions.
“The breach was admitted by Car #78 and the Stewards imposed a 15 second post-Race Time Penalty on Car #78.”