The runaway Formula One championship leader set a best time of one minute and 05.742 seconds with his final lap of the session around Spielberg's scenic Red Bull Ring at the start of the season's second sprint weekend.
Ferrari's Carlos Sainz was 0.241 slower on the softs with teammate Charles Leclerc third and 0.270 off the pace after his final effort.
Mercedes' seven-times world champion Lewis Hamilton was fourth, also on softs after doing his long run on hards, with Verstappen's teammate and closest title rival Sergio Perez fifth, on mediums.
The strategy pointed to Mercedes saving medium tyres for Sunday and Red Bull, who have won every race this season, keeping hards in reserve.
Perez, 69 points behind Verstappen after eight of 22 races, had stayed away from the circuit on Thursday after reporting sick.
Canadian Lance Stroll was sixth on softs for Aston Martin ahead of Haas's Kevin Magnussen and Aston's Fernando Alonso eighth on mediums.
The session was the sole practice of the weekend with qualifying for Sunday's race following on Friday, with Saturday a standalone sprint day featuring qualifying for the 100km race that follows.
