The Clogher rider took a narrow victory over compatriot Alastair Seeley after 10 laps, with Dublin's Jack Kennedy fourth and David Allingham in sixth.
Seeley is unable to score championship points onhis Spirit Moto2 machine.
Farmer now lies second in the standings on 145 points, five behind Tarran Mackenzie, who has taken up Danny Kent's ride in the Moto2 MotoGP series.
Allingham is third on 134 points, followed by Carrickfergus rider Andrew Irwin on 115 and Kennedy with 100.
The feature Supersport event will take place on Sunday.
Be Wiser Ducati pilot Glenn Irwin misses the meeting through injuries sustained in a practice crash at Knockhill but Northern Ireland riders Michael Laverty, Andy Reid and Josh Elliott will take part in Sunday's two Superbike outings.
Reid has been called up to replace Davide Giugliano in the Tyco BMW team for the remainder of the season, while Elliott stands in for the injured Christian Iddon for this round.
Elliott is also set to take in this weekend's Superstock 1000cc races, along with MD Racing representative Carl Phillips.
Keith Farmer followed up his double at Knockhill by winning the Supersport sprint race at Snetterton on Saturday.