Brown had produced an impressive come from behind drive to win Race 2 on the road at Sandown, having started from fifth on the grid.
The Toowoomba racer leapt to second on the opening lap before taking the lead with a slick pass on Nick Rowe on the back straight.
Once in front he held the position to the flag from Denton, who dived by Rowe at Turn 9 on the final lap.
However, a post-race inspection of the #99 Team BRM entry revealed a breach of the technical regulations promoting Denton to victory from Rowe and Jordan Love.
Harry Hayek has been awarded fourth ahead of Jack Smith and Tyler Everingham.
Brown's exclusion will provide a much needed boost for Rowe's title hopes after finishing Friday's opening race in fifth.
Rowe is just 28 points adrift of Brown ahead of the weekend's third 13 lap race on Sunday at 0905 local time.
Toyota 86 Racing Series
Starting from second, the Formula 4 racer moved into the lead when pole-sitter Adam Gowans lost control at Turn 6 and plunged into the tyre wall on the opening lap.
Once ahead, Brown was rarely threatened on his way to the chequered flag from Luke King and Tim Brook.
Aaron Seton managed to bring his Sci-Fleet Hino Toyota 86 home in fourth ahead of David Sieders and top guest driver Steven Johnson.
Series leader Cameron Hill finished seventh despite a tangle with Josh Hunter, while Dylan Gulson, Jake Klein and Leanne Tander completed the top 10.
Two-time Bathurst 1000 winner Tony Longhurst finished 19th on his series debut.
King added his name to the winners list in the second race courtesy of a late move on long time leader Brown.
After winning the opening heat, the Queenslander appeared set for another victory having led until the penultimate lap.
However, Brown ran wide at Turn 1 which allowed King through to the lead. The error was severely punished with Seton, Sieders and Johnson following King through.
King held his nerve in the closing stages to take the victory from Seton, Sieders, Johnson and Brown.
Gulson, Grice, Tander and Hunter filled positions sixth through 10th.
Hill's difficult day continued when he misjudged his braking for Turn 1 and clattered into the side of Brook on lap five, putting the latter out of the race.
The former Australian Formula Ford Series winner managed to continue on to 15th at the finish in front of Longhurst.
The 33 car field will line up for a final 11 lap race on Sunday at 1015 local time.