Thirty-nine-year-old Leeds-based manager O'Malley beat his closest rival, Londoner Magd Mohaffel, up the hill by 1.3s. O'Malley now leads Mohaffel overall by two points.
Kent-based underwriter Mark Figes was third quickest at Harewood while Aintree podium finisher Ross Culver placed fourth despite a gearbox problem.
Both Academy groups will be taking centre stage at the Caterham 7 Jubilee meeting at Donington Park, the venue for their maiden circuit race on 2/3 Ju