It commenced on 5 April at Oulton Park's Easter Monday meeting and ended on 26 September at Brands Hatch after 10 rounds and 25 races, held in the United Kingdom and the Netherlands.
Malvern, who had previously been a part of the Jamun team working as a mechanic for 2008 runner-up Tim Blanchard, won only two races during the season but with 22 top-five finishes, he outscored Pye by a solitary point on total scores.
Daniel Cammish took third place in the championship standings, having started the season in Kevin Mills Racing's Spectrum and ended it as a twice race-winner, at the wheel of one of JTR's trio of Mygales.
Tristan Mingay won the Scholarship Class championship for older machinery, beating his only other full-season rival Luke Williams by 76 points.
Both drivers won the class on eleven occasions, but with more finishes, Mingay held a comfortable margin and duly claimed the title with a race to spare.