The young men's pursuit team of Sam Welsford, Alex Porter, Miles Scotson and Rohan Wight took gold from Denmark finishing in 3 minutes 57.461 seconds.
"To come away with the gold is a great feeling, we all worked really hard for this and to get the result is amazing, especially with us being such a young team," Porter said.
Rohan Wight debuted with the squad at the World Cup.
"I'm super happy with the times, I hadn't gone sub four minutes before so to do it twice in one day was fantastic," he said.
Earlier in the day the four booked their spot in the final clocking up 3mins 56.517secs to Germany's 4:00.322.
"Winning the overall series, just shows the depth and consistency of the entire squad which is a really good sign with Rio approaching," Porter said.
Bronze went to Great Britain in 3mins 59.706secs.
At just his third World Cup, Patrick Constable took the biggest win of his career with a gold in the sprint. He defeated Chao Xu (China) in two heats racing both from the front in the final lap.
"It's huge, I'm stoked I could get the job done and end up on the top step," said Constable after his breakthrough win.
"I've just focused on stepping up again this year, 12 months is a long time in sprinting, but I'm happy with where I'm heading. That was always my big goal, being consistent at this level. All the best guys in the world do it so well, and I want to be competitive at the top level."" he said.
Stephanie Morton took silver in the keirin, her fourth this season.
"It's been awesome. It's the most successful World Cup season I have had so cant complain at all," she said.
"I was buzzing for the final after just watching Pat win the sprint. I had to go the long way around and copped a couple of hooks so that wasn't ideal.
"It turned into a long sprint but I put on the after burners and was happy to walk away with a silver."
Over the series, Australia claimed a total of 15 medals, five of them gold, seven silver and three bronze. The cyclists now focus on the 2016 Subaru Track National Championships February 3rd-6th in Adelaide and then the 2016 UCI Track World Championships in London in March.