Marc Marquez led the first half of the 45-minute session with an early benchmark lap of 1m48.804s.
Dovizioso became the second rider to dip below the 1m49s barrier when he went 0.001s quicker than Marquez with 20 minutes remaining, and the factory Ducati rider did not lose the lead thereafter.
There was a brief moment when the top three spots were separated by 0.001s when Maverick Vinales set the same time as Dovizioso, before the latter then went eight tenths clear.
Dovizioso ultimately topped the session with a 1m48.020s, with only his future team-mate Danilo Petrucci managing to get close to him with a 1m48.210s.
Jack Miller and Jorge Lorenzo completed the top four, but both ended up more than seven tenths off the pace.
Vinales and Marquez were best of the rest in fifth and sixth respectively, with two more Yamaha riders - Valentino Rossi and Johann Zarco - seventh and eighth.
Cal Crutchlow finished ninth ahead of Andrea Iannone, who had a small mechanical issue with his clutch cover during the session, and Alex Rins, Pol Espargaro and his brother Aleix.
Xavier Simeon had a dramatic end to the session - he is riding Tito Rabat's GP17 for the second weekend in a row - as his engine appeared to explode late-on at Turn 1 in a huge cloud of smoke.
Avintia's MotoGP debutant Jordi Torres finished 24th, 4.8s slower than Dovizioso.