Lynn came out on top, which was a great fillip for the British driver after his big crash in the feature at Teretonga while fighting for the lead with Serralles.
"This is what should have happened at Teretonga but it was a hard race," said Lynn. "I was defending the whole race, to be honest.
"I was quick and pulling away from the rest of the field but Lucas came with me. He put me under a lot of pressure and I was working really, really hard all through the race."
Defending TRS champion Nick Cassidy is still looking for his first race win but finished the weekend on the podium twice and set a new lap record in the third race.
Auer continued his good form from the opening round at Teretonga in race one on Saturday where he dominated the field to win from Cassidy and Bruno Bonifacio.
"It wasn't as easy as it looked. It got a bit slippery towards the end of the race so I didn't push too hard. It's a small track that's quite twisty but I like it," said Auer.
Championship leader after the first round, Serralles was hampered by problems in qualifying and couldn't improve on his sixth place start.
Race two was a reverse grid top six affair and Serralles made the most of his start from pole to lead the field into the first corner and was never really challenged for the rest of the race.
Kiwi driver Damon Leitch slotted in behind the leader, Cassidy passed Bonifacio to settle into third, and that was the race order as they crossed the finish line.
The series now heads to Taupo for round three next weekend.
Australian V8 Supercar driver Jason Bargwanna increased his lead in the NZV8s, winning two of three races in his new generation V8.
TRS points
After round two
1 Lucas Auer, Austria 382
2 Felix Serralles, Puerto Rico 376
3 Nick Cassidy, New Zealand 329
4 Pipo Derani, Brazil 289
5 Damon Leitch, New Zealand 282
= Alex Lynn, UK 282
7 Stejin Schothorst, Netherlands 270
8 Bruno Bonifacio, Brazil 259.
