Hughes, who entered the round with a slender lead over Daniel Rochford in the standings, had a consistent weekend before finishing fifth in the final race to seal the title.
It's the second consecutive year that the JAM Racing outfit has won the prestigious title, it's also the third consecutive year that the championship has been won by a driver in a Kosmic chassis.
“This win is a reward for everyone's hard work at JAM Racing, to have won the past two titles is just a great team effort,” said Hughes.
“The championship this year has been the toughest that I've ever been involved in, every time you hit the track you knew you're in for a real fight and that showed again this weekend.
“It's an amazing feeling to have got this championship and now have my name alongside some of the great names in Australian motorsport on the James Courtney trophy.”
The battle for the Pro Gearbox title also went down to the wire between Patrizicorse Speedcafe.com backed driver Kyle Ensbey and Vodafone Energy Corse Australia driver Chris Hays.
When Ensbey came together with reigning champion, Tyler Greenbury, in the opening final it all but ended his championship hopes. Greenbury was excluded from the race for his part in the incident.
From there, Hays went on to win both 27-lap encounters to secure the Pro Gearbox (KZ2) championship, along with the $10,000 towards an overseas CIK event that goes with it. His name will also be etched on the John Pizarro perpetual trophy.
In the Pro Junior (KF3) ranks Hill entered the final day of competition with an insurmountable lead before signing off with a pair of victories on the Port Melbourne circuit.
Hill led home Thomas Randle and Liam McLellan, who was making his debut in the category.