The Welshman excelled in qualifying to put his Calsonic Nissan GT-R NISMO GT500 on the front row.
Mardenborough started the race in wet conditions, chasing his flat-mate and rival Nick Cassidy for the lead.
The race started under safety car conditions after a rain shower but quickly dried with Mardenborough stopping a lap later than Cassidy. The two continued to battle for the lead with Mardenborough stopping for the driver change six laps later and maintaining a handy lead.
On the last flying lap before his stop, Mardenborough set the fastest lap of the race – more than 2/10ths of a second faster than the entire GT500 field.
Hiro Yasuda took over and looked set to claim the first podium of the season for the Calsonic machine when they suffered a fuel system issue with three laps remaining and were forced out of the race.
Ronnie Quintarelli and Tsugio Matsuda took a ninth-place finish in Thailand after electing to start on slick tyres at the start of the race.
“It took about five laps for the road surface to dry but after it did the tyres gripped really well,” Quintarelli said.
“I’m glad we could make it through that rough beginning to the race and come back to finish in ninth.
“Ultimately, we wanted to get some points and I think the two points we got today were really essential. We will be heading into Motegi with an eight-point difference to the leader and the potential to take the championship.
“We’ve been able to earn points in every race this season, but we are yet to take a win. To begin with, we will be aiming for a victory and won’t stop fighting until the end.”
Satoshi Motoyama and Katsumasa Chiyo finished 10th in Thailand with Daiki Sasaki and JP de Oliveira suffering an early delay with a driveline issue at the start. The Brazillian/Japanese combination rejoined the race 32 laps behind but completed a race finish.
The final round of the Super GT Championship will be held at Twin-Ring Motegi on November 12 and shown live on NISMO.tv