Guintoli beat his team-mate to the chequered flag in the first race with his Northern Irish counterpart securing the second.
Guintoli's victory in race one was the fourth of his career, and he secured it by overtaking Laverty on lap 15 and holding off the rest of the field, leaving Laverty and another Aprilia rider, Michel Fabrizio, to battle it out for second.
Laverty waited until the last lap to make the perfect move on the Italian at Lukey Heights to secure the runners-up spot.
Ducati Alstare rider Carlos Checa - who secured pole on Saturday - exited the race after lap 14 after colliding with Marco Melandri, with his injuries forcing him out of the second race.
Laverty ended the second race strongly to join his team-mate at the top of the standings, while Melandri finished third behind Guintoli.
Laverty recorded a fastest lap of one minute 31.168 seconds on lap 20 to pass Melandri and Guintoli to move into first, where he stayed.