World championship leader Brad Binder ran a perfect three final sectors to have enough in hand to claim Moto3 pole position at Misano - despite being mired in traffic.
The Red Bull KTM riders final lap of 1m 42.398 was heading towards being Moto3's first 1m 41 lap of Misano when Binder found traffic, racing through any gaps available and still bettering Enea Bastianini's old pole record in the process.
Lining up next to the Silverstone winner is last season's pole man and winner Bastianini, who also improved on his last lap aboard the Gresini Honda to move into second.
The final front row spot goes to fellow Italian Nicolo Bulega. The local rookie rider was last out for his final run aboard his KTM but did not improve, the Sky Racing VR46 team rider had already shown enough pace to keep third.
Jakub Kornfeil was also on the pace, his best effort saw hi climb from ninth to second, and held well as the final flurry of bikes crossed the line to give the Drive M7 SIC rider fourth.
Jorge Navarro looked keen to get near the front on the grid to try to reduce Binder's lead on Sunday, but the Estrella Galicia rider was one of three riders to crash in the final minute of the session (Along with Jorge Martin and Lorenzo Dalla Porta) leaving him watching as his time fell to fifth.
Next to him on the grid in sixth will be his team-mate Aron Canet.
Philipp Oettl put in a solid performance for his Schedl GP Racing team to claim seventh, Hiroki Ono had a good run for eighth for Honda Team Asia, Juanfran Guevara also surprised to take ninth with RBA Racing.
The Second Gresini piloted by Fabio Di Giannantonio followed his team-mate on track to improve and secure the final top ten spot.
On the eve of their 100th grand prix the best Mahindra on the grid is faller Jorge Martin, who hit the back of his Aspar team-mate Bagnaia and looked to have pain in his ankles after his crash, who will start twelfth.
Niccolo Antonelli was looking for a positive performance after being disqualified in Silverstone (as he and his bike did not meet the required weight limit) but it was not to be with the Ongetta-Rivacold rider - only managing 14th on the grid.
Leopard rider Joan Mir had topped practice but spent much of the session in the pits with bike issues before returning for 16th for the Leopard Racing team.
Away from the wet the Peugeot Mahindra team found the going tough once again. Albert Arenas finished top of the Saxoprint riders in 26th, John McPhee struggled to be fast and stay within the track limits and after having several laps cancelled finished his session 29th.
It took just minutes for Fabio Spirnelli to become the first faller, looking a little battered and winded after being thrown from his Mahindra. Andrea Migno was the next to exit heading into the final fifteen minutes.
Mahindra rider Stefano Manzi returns again as a wild-card following his frantic fourth at Silverstone and will again be looking to progress from the back, though from an improved 20th.
He is joined by Alex Fabbari, A local San Marino rider, who makes his debut with Minimoto Portomaggiore in 35th on the grid.