Fraser trailed Tyler Everingham to the chequered flag, taken under Safety Car, but a penalty for a collision with a backmarker demoted the MW Motorsport driver outside the top 15.
Zak Best was classified second from Dean Fiore in a race that ultimately ran to time instead of its originally scheduled 22 laps.
Matt Payne had qualified on pole but was relegated three places after it was deemed his fastest lap in qualifying was set under yellow flags.
Everingham started from pole as a result, getting away into a clear lead as the race began, while a stall at the back immediately drew the Safety Car.
Ninth placed Maxwell was left stranded on the grid, though was avoided by the field before getting going just as the Safety Car was deployed.
At Turn 1, Blake Fardell and Jim Pollicina got together, the latter in deep, locking the brakes to spear into Cameron Crick, and in turn into Fardell, who just about had the front passenger door plucked from the car.
He was able to circle back to the pits to have the issue rectified just as the lights were extinguished on the Safety Car, exiting the lane as Everingham led the field back to green.
It was a good jump from the Altima driver, heading the field once again as they started Lap 3, with Matt Chahda second from Payne and Fiore.
A moment for Cameron Hill, which had a hint of assistance to it, left the Triple Eight driver pointing the wrong way exiting Turn 4 soon after the restart, plummeting the man who sat second in the series well down the order.
Aaron Seton was left with nowhere to go into Dandenong Road, forcing him to spear off the road and skate through the gravel trap before rejoining.
As that was happened, race control confirmed a 15 second penalty for Pollicina for his role in the opening-corner melee.
In the lead, Everingham began to edge clear, despite a bit outside-front lock-up into Turn 1.
Payne's pulling to the side on the front straight with his splitter full of mud and grass but was able to recover to the pits.
Jack Perkins was also caught up in the scuffle, slipping to 12th as a result while Payne was slapped with a 15s penalty for his role in the original clash.
Through it all, Everingham remained clear out front, his lead extending to 3.5s over Fiore in second and Zak Best in third.
Race control announced the race was declared wet on Lap 9, with light rain beginning to fall.
Leader Everingham lost almost the entirety of his advantage when he came across Garry Hills at Turn 4, the pair making contact and damaging the splitter on the Image Racing car.
It was a defining moment as it resulted in a 15 second penalty for the pole sitter at a time when his lead had evaporated.
That afforded Fiore an opportunity to attack, only instead lose out to Best and then Fraser.
Best than ran wide at Turn 1 as they started Lap 13 to open the door and allow Fraser through.
With eight laps remaining, Chris Smerdon found himself beached at Dandenong Road to draw the Safety Car.
Everingham led the field to the restart in what would be a quickfire run to the time certain finish.
It was a brief resumption as Strong stopped on the front straight to necessitate the Safety Car once more.
The field did not immediately receive the chequered flag, instead touring around behind the Safety Car one last time.
With Fraser locked on to Everingham's bumper, the Triple Eight driver was classified the winner from Best and Fiore.
Kai Allen headed the Super3 field, climbing to seventh across the line but moving up to sixth once Everingham's penalty was taken into account.
Indeed, the pole sitter fell to 19th behind Seton in a race he'd otherwise controlled.
The combined Super2 and Super3 field returns to the circuit at 10:15 AEST on Sunday for qualifying for Race 2 of the weekend, which follows at 15:00.