With team owner and mentor Valentino Rossi in attendance at the Red Bull Ring this weekend, Bezzecchi set a new lap record on the revised Spielberg layout to lead Friday's second session by 0.044s.
Bezzecchi did stop on track on the run down to Turn 4 at the end of the session having run out of fuel before the chequered flag.
He headed Aprilia's Maverick Vinales and championship leader Francesco Bagnaia on the factory Ducati, while Fabio Quartararo bagged a place in qualifying Q2 on his factory Yamaha.
The hour-long afternoon session was delayed by 10 minutes due to an incident in the preceding Moto2 FP2 leading to an air fence needing to be replaced.
When the action got underway, the track was a hive of activity as rain threatened above the Styrian hills.
Ducati's Bagnaia set the early pace with a 1m30.511s five minutes in before Vinales took over with a 1m29.618s on a fresh medium rear tyre.
Bezzecchi took his first trip to the top of the order with a 1m29.569s moments later, also on a medium rear, before KTM's Brad Binder went quicker with a 1m29.559s on a fresh soft tyre.
With just over 10 minutes of the session gone, Bezzecchi found a 1m29.450s, which would stand as the benchmark until Vinales fitted a fresh soft rear tyre 12 minutes later.
The Aprilia rider stormed clear of the pack with a 1m29.075s and would go unchallenged until the final 10 minutes.
Just over halfway into second practice, rain flags began to wave as spots sprinkled parts of the track.
The rain never amounted to much and faster laps continued to flow in, with Bagnaia going top with a 1m28.821s with just under nine minutes left.
But a 1m28.533s from Bezzecchi on his year-old VR46 Ducati would prove to be the time that sealed top spot, as Vinales slotted in between him and Bagnaia.
Binder was fourth at the end from the Pramac pair of Johann Zarco and Jorge Martin, while British GP winner Aleix Espargaro made a late charge up to seventh on his Aprilia to secure a direct Q2 place for Saturday morning.
Alex Marquez was eighth on his Gresini Ducati from Quartararo and RNF Aprilia's Miguel Oliveira.
Luca Marini just missed out on a Q2 place by 0.026s on the second of the VR46 Ducatis, while Marc Marquez was denied a top-10 spot after a late run-in with Pol Espargaro.
Having been inside the top 10 in the closing stages of second practice, Marquez was forced to abort a good lap having been caught out by a touring Tech3 of Espargaro.
Both will face Q1 on Saturday morning, while the stewards are currently investigating the incident.
Joining them in Q1 will be the factory Ducati of Enea Bastianini, who was left 16th after a late Turn 2 crash, while Jack Miller couldn't match team-mate Binder's form in 14th.
