Dovizioso clocked a time of 1:23.617 to finish 0.238s faster than Ducati team-mate Andrea Iannone as Ducati exploited its speed advantage at the Red Bull Ring.
Dovizioso was 0.854s quicker than third-placed rider Maverick Vinales, representing Suzuki, who wound up just 0.012s ahead of Yamaha's Valentino Rossi.
LCR Honda's Cal Crutchlow was fifth quickest, in front of Danilo Petrucci and Hector Barbera, the pair both using satellite Ducati machinery.
Jorge Lorenzo was a low-key eighth, having set the same time as Ducati wild card rider Michele Pirro.
Repsol Honda had a troublesome showing, with Marc Marquez managing only 10th as Dani Pedrosa, who crashed at high speed in the first session, down in 19th position.
The only rider to encounter trouble was Suzuki's Aleix Espargaro, who tumbled out of proceedings at Turn 8.
The third practice session will begin on Saturday at 09:55 local time
PRACTICE TWO TIMES
POS RIDER TEAM BIKE TIME GAP LAPS
1 Andrea Dovizioso Ducati Ducati 1m23.617s – 21
2 Andrea Iannone Ducati Ducati 1m23.855s 0.238s 22
3 Maverick Vinales Suzuki Suzuki 1m24.471s 0.854s 21
4 Valentino Rossi Yamaha Yamaha 1m24.483s 0.866s 24
5 Cal Crutchlow LCR Honda Honda 1m24.688s 1.071s 22
6 Danilo Petrucci Pramac Ducati Ducati 1m24.866s 1.249s 24
7 Hector Barbera Avintia Ducati Ducati 1m24.956s 1.339s 20
8 Jorge Lorenzo Yamaha Yamaha 1m24.988s 1.371s 22
9 Michele Pirro Ducati Ducati 1m24.988s 1.371s 23
10 Marc Marquez Honda Honda 1m25.039s 1.422s 22
11 Yonny Hernandez Aspar Ducati Ducati 1m25.042s 1.425s 23
12 Scott Redding Pramac Ducati Ducati 1m25.140s 1.523s 22
13 Pol Espargaro Tech3 Yamaha Yamaha 1m25.221s 1.604s 22
14 Jack Miller Marc VDS Honda Honda 1m25.321s 1.704s 20
15 Tito Rabat Marc VDS Honda Honda 1m25.770s 2.153s 29
16 Alvaro Bautista Aprilia Aprilia 1m25.882s 2.265s 24
17 Bradley Smith Tech3 Yamaha Yamaha 1m25.941s 2.324s 27
18 Aleix Espargaro Suzuki Suzuki 1m25.945s 2.328s 4
19 Dani Pedrosa Honda Honda 1m26.130s 2.513s 21
20 Stefan Bradl Aprilia Aprilia 1m26.149s 2.532s 22
21 Eugene Laverty Aspar Ducati Ducati 1m26.469s 2.852s 20
22 Loris Baz Avintia Ducati Ducati 1m26.491s 2.874s 22