The pair emerged victorious after two race suspensions and a late safety car, heading the pack by 4.1 seconds at the end of 78 laps.
Starting from the outside of the second row, an excellent opening stint from Bates saw Gaunt take control with 50 laps in the books.
Sixth when he climbed aboard, Gaunt charged his way into the lead just two laps later as those around him stopped, controlling the race to the chequered flag.
The GT4 class was taken out by the all-American pairing of Daren Jorgensen and Brett Strom in a BMW M4 GT4.
They fended off David Crampton and Trent Harrison in their KTM X-Bow GT4 by just 0.2s in a thrilling finale, the BMW duo having headed the class battle throughout the race.
A crash for Saturday’s Trophy Series sensation Rio Nugara on Lap 39 initially drew the safety car as the Ginetta G55 GT4 found the tyre wall at Lukey Heights, before officials elected to suspend the race.
Glen Wood and Vince Tesoriero were also retirements after their KTM X-Bow GT4 tagged the wall at Turn 1, the class leading Aston Martin Vantage GT4 of Jeremy Gray and Andrew Miedecke replicating the KTM seconds later.
It saw officials again suspend the race to affect repairs to the tyre barrier, setting up an incredibly dramatic finale.
The pole sitting Porsche 911 GT3 R of Liam Talbot and John Martin had dominated proceedings until a late incident changed the complexion of the incredible race once again.
The Walkinshaw GT3 entry was forced out on Lap 62 which it picked up damage to the radiators after running wide at the first turn.
It was a devastating end for the team having earlier watched Martin’s mesmerising opening stint which saw him more than two seconds a lap faster than his rivals.
The Eggleston Motorsport Mercedes-AMG GT3 also looked a strong contender for the race win, holding a lap advantage before a late penalty saw Peter Hackett and Jake Fouracre home in eleventh.
Through the drama, Bates and Gaunt proved a rock solid combination, using the car’s pace coupled with the right strategy calls throughout what proved to be a time-certain race to see the chequered flag first.
It’s a result that rockets Bates to the top of the CAMS Australian GT Championship points standings.
As the race also formed part of the CAMS Australian Endurance Championship, Bates and Gaunt also received a hefty 300-point boost in their title hopes on that front.
The Audi pair now sit third in the Australian Endurance Championship standings, just 42-points away from Tony D’Alberto and Max Twigg, who safeguarded their points advantage with another stellar drive to the podium.
The Mercedes-AMG GT3 pairing crossed the line third, their fourth consecutive podium in the competition, an incredible run of results that stretches back to Hampton Downs at the tail end of the 2017 season.
Second place went to the BMW Team SRM M6 GT3 piloted by Steve Richards and Michael Almond after a faultless performance from both drivers.
An impressive opening stint for Almond saw the BMW in contention throughout the race before Richards picked off his rivals to record the squad’s second successive Australian Endurance Championship podium.
They now trail Twigg and D’Alberto by 36-points with one Australian Endurance Championship round remaining.
The CAMS Australian GT Championship now heads to Sydney Motorsport Park on August 3-4, before the season finale in Hampton Downs in October.
The Hampton Downs event will double as the third and final round of the CAMS Australian Endurance Championship, setting up an exciting climax to the 2018 season.
Results: Australian GT Championship, Round 4, Phillip Island 101
Pos Competitor/Team Driver Vehicle Laps Race Time Class
1 KFC/Ctech Laser/Moveitnet/B&B Tony Bates Audi R8 LMS 78 3:27:31.731 CH
2 BMW Team SRM Steve Richards BMW M6 GT3 78 3:27:35.893 CH
3 WM Waste Management Max Twigg Mercedes-AMG GT3 78 3:27:36.790 CH
4 International Motorsport Andrew Fawcet Audi R8 LMS 78 3:27:38.312 CH
5 Valvoline Geoff Emery Audi R8 LMS 78 3:27:38.469 CH
6 Total Oil/Opti-Coat/Boost Mobile Fraser Ross McLaren 650S GT3 78 3:27:39.917 CH
7 Scott Taylor Motorsport Scott Taylor Mercedes-AMG GT3 78 3:27:41.242 CH
8 Wall Racing Adrian Deitz Lamborghini Huracan GT3 78 3:27:41.334 CH
9 Objective Racing Tony Walls McLaren 650S GT3 78 3:27:49.182 CH
10 The Bend Motor Sport Park Yasser Shahin Mercedes-AMG GT3 78 3:28:19.924 CH
11 Eggleston Motorsport Peter Hackett Mercedes-AMG GT3 78 3:28:20.412 CH
12 YNA Autosport Duvashen Padayachee McLaren 650S GT3 75 3:27:49.321 CH
13 LOCAL Search by MARC Cars Adam Hargraves MARC Mazda V8 75 3:28:47.033 MA
14 RHC Jorgensen – Strom by MARC Cars Daren Jorgensen BMW M4 GT4 73 3:27:45.706 GT4
15 Vantage Freight/M Motorsport David Crampton KTM X-Bow GT4 73 3:27:45.964 GT4
16 Ah Apartments Ash Samadi Audi R8 LMS 73 3:27:55.888 CH
Walkinshaw GT3 Liam Talbot Porsche 911 GT3 R 61 2:57:21.700 CH
Forum Group/M Motorsport Vince Tesoriero KTM X-Bow GT4 48 1:51:33.688 GT4
JMG/Bilstein Jeremy Gray Aston Martin Vantage GT4 47 1:51:39.644 GT4
Hogs Breath Café/Griffith Corporation Mark Griffith Ginetta G55 GT4 39 1:10:08.501 GT4
Mariani Beef Jerky Tony Quinn McLaren 650S GT3 7 0:25:59.996 CH
Points Standings: Australian Endurance Championship (2 of 3 rounds)
1. Max Twigg/Tony D’Alberto, 551-points
2. Steve Richards/Michael Almond, 515
3. Tony Bates/Daniel Gaunt, 509
Points Standings: Australian GT Championship (4 of 6 rounds)
1. Tony Bates, 712-points
2. Fraser Ross, 687
3. Steve Richards, 681
Points Standings: Australian GT Championship GT4 (4 of 6 rounds)
1. Jeremy Gray, 707-points
2. David Crampton/Trent Harrison, 534
3. Justin McMillan, 476
Source. Australian GT Championship