Verstappen's title rival and defending champion Lewis Hamilton was third in the early run before the Mercedes driver finished fourth later in the day.
His teammate Valtteri Bottas, however, was handed a three-place grid penalty and accused of "dangerous driving" by stewards after a bizarre spin in the pit lane following a change on to hard tyres.
The Finn simulated a race start but spun sideways just avoiding a collision with the pit wall and resulting in the McLaren mechanics helping him straighten up and leave the pits.
McLaren duly reported the incident, complaining that it was "absolutely ridiculous... he could have taken our guys out".
Stewards subsequently handed Bottas, who could only clock the twelfth fastest time, a three-place grid drop for Sunday's race, along with two penalty points on his licence.
"When [Bottas] pulled away from his designated pitstop position, he lost control of the car when he turned into the fast lane," said the stewards in their ruling.
"He oversteered, spun and came to a stop across the fast lane near the McLaren pits.
"During the hearing [Bottas] stated that in the past they have been losing time in the pit departure. So they tried something new, which was to leave in second gear.
"As a result, the wheel spin was much higher and the result unexpected. Therefore he didn't manage to control the car properly into the fast lane.
"This has to be considered as potentially dangerous driving, especially as personnel were around in the pit lane."
Alpha Tauri's Pierre Gasly was unable to repeat his opening session, where he claimed second, due to an issue with his engine.
Verstappen, 23, goes into Sunday's contest with a 12-point lead over seven-time champion Hamilton, who had his best time scratched out by officials for leaving the track.
"Lewis drove the best time but it was cancelled, so the performances are a bit different to what we're seeing on the timings," Verstappen said.
The Dutchman, who switched to soft tyres midway through the first session in Austria, was in no mood to give his rivals any early hope as he blazed round in 1min 05.910 sec.
Verstappen's team-mate Sergio Perez, who is third in the overall standings, could only record a ninth-quickest pace.
"We are without doubt this weekend's hunters," Mercedes team principal Toto Wolff said.
Ferrari's recent woes coming off a pointless finish at the French Grand Prix continued as Carlos Sainz spun across at turn one before trundling in 11th place in the two runs.
The final practice run starts on Saturday before the qualifying run later in the day with storms forecast near the Austrian Alps.