The Spanish rider had started the campaign without a contract, deputising for the team's injured rider, James Haydon, in the opening two rounds, but he accumulated points and earned the ride for the rest of the season.
Lavilla's challenge intensified in the second half of the season in which he enjoyed a brilliant run of six victories and five second placings in 11 outings.
Haydon, riding for Rizla Suzuki, had started from pole, but he was beaten away from the line by the determined Haslam, who led for four laps before Lavilla charged through at Druids, to take victory by a third of a second.
Ryuichi Kiyonari, his only rival for the crown, was back in fourth place, behind Haydon, and that meant Lavilla needed only a single point from the second race of the day to secure his first major title. Lavilla went on to shatter the outright lap record as he finished in second place behind Haslam to take the champion's trophy.
"It is a great feeling but I did not expect to be standing here at the start of the season. My thanks to the team," Lavilla said. "After the summer break we raced on circuits I knew and started winning regularly, taking points back from the Hondas. It has been a great year and we have finished it well."
Kiyonari was again fourth in the second race, this time finishing adrift of Steve Plater riding the Hydrex Honda.
At Magny-Cours in France, James Toseland's attempt to secure third in the World Superbike Championship standings ended when he finished sixth in the second race of the final round.
Toseland had finished third in race one on his Ducati Xerox as Japan's Noriyuki Haga, third in the championship going into yesterday's races, crashed out on the Yamaha Motor Italia machine. But things did not go so well for Toseland second time out.
The race one winner, Chris Vermeulen, did not finish the second race on his Ten Kate Honda, which was won by Lorenzo Lanzi on the Caracchi Ducati. Second went to Yukio Kagayama, who finished the series just two points adrift of Toseland in fifth.
Haga confirmed third in the championship standings after finishing behind Kagayama in the second race. Fourth went to the new world champion, Troy Corser, who had taken the title from Toseland, the defending champion, in the previous round and finished 54 points clear of Vermeulen.