Tauranga's Sam Meech was fifth overall after a 16th placing.
It was a terrific end to a long season for Saunders that has seen him on the road for nearly four months. He was eighth at the world championships in Croatia and fourth at the world championships test event in Aarhus and his results could be enough to see him elevated to the top-tier NZL Sailing Team.
"This is my first proper win in the Laser fleet so I am really happy," Saunders said.
"It's been quite a long season, so to finish it off like this means a lot. I will have a nice break when I get home and reset and go from there. There was obviously a lot of rain and there was poor visibility. It was probably the worst conditions I have sailed in. Going upwind you couldn't see the top mark and you could barely see the rest of the fleet. It was pretty strange in that sense but you just had to work with what you got."
Maloney and Meech did that better than anyone in the 49erFX fleet today, easily winning both races to finish nine points ahead of the German pair of Victoria Jurczok and Anika Lorenz who had started the day level on points.
The Olympic silver medallists had a poor start to the regatta, ending the first day in seventh in the small fleet of 12 boats, but roared back with five wins and a second placing in the last six races.
"It's cool to win the regatta, the first regatta at the Olympic venue," Meech said. "But it will get more and more competitive over coming years with the fleet growing and I think everyone here was learning about the venue, just figuring things out."
One thing all of the New Zealand sailors worked out was that it rains a lot in Japan in October, and a second typhoon rolled through bringing torrential rain and gusts in excess of 20 knots.
"It was lovely," Maloney said with a wry smile.
"We like a good bit of rain coming from New Zealand. Molly almost pulled the pin this morning. She keeps warning me she doesn't sail in the rain but we survived."