Honda MotoGP rider Marc Marquez secured pole position for Sunday's Czech Grand Prix by 2.5 seconds at a drying Brno circuit after a controversial run-in with Alex Rins.
After tackling their first runs on wets in Q2, several riders switched to slicks during the mid-session lull.
Having advanced from Q1, the KTMs of Johann Zarco and Pol Espargaro held a shock one-two early on and were two of a handful of riders that stayed on wets until the end.
Their decision appeared to have paid off as it started to rain again during the final few minutes.
But Marquez mastered the conditions and, despite running on slicks, made two massive improvements in a row, ending the session with a 2m02.753s while the rest of the field could not break the 2m05s barrier.
Pramac Ducati's Jack Miller was another rider to improve on slicks and but his qualifying ended in a crash at Turn 14, but not before he secured second.
Zarco held on to a sensational third on his first Q2 appearance of the season while Espargaro took fifth, the pair sandwiching Andrea Dovizioso's Ducati.
Rins qualified sixth after the Suzuki rider was involved in a controversial incident with Marquez.
Rins aggressively overtook Marquez as both returned to the pits after their first runs, but Marquez then nudged Rins' bike as they were running side-by-side in the pits.
Valentino Rossi did not switch to slicks and was seventh, and fastest of the Yamahas, followed by Danilo Petrucci (Ducati), Maverick Vinales (Yamaha) and Fabio Quartararo (Petronas Yamaha).
LCR rider Cal Crutchlow was the second-best Honda in 11th, 4.3s slower than Marquez, as Franco Morbidelli (Petronas) qualified 12th and last of the Q2 runners.
Crutchlow's LCR team-mate Nakagami was fastest of those eliminated in the first part of qualifying behind the two KTMs, and will line up 13th ahead of Pramac Ducati rider Francesco Bagnaia.
Suzuki wildcard Sylvain Guintoli, who impressed in the wet FP3 and FP4 sessions, will start 15th, ahead of the Tech3 KTM of Miguel Oliveira.
Honda rider Stefan Bradl, who is standing in for the injured Jorge Lorenzo at the works squad, only secured 17th on the grid ahead of the top Aprilia of Aleix Espargaro and Suzuki's Joan Mir.
Karel Abraham (Avintia Ducati) will start his home grand prix from 20th.
Provisional starting grid
|2||Jack Miller||Pramac Ducati||Ducati||2.524s|
|10||Fabio Quartararo||Petronas Yamaha||Yamaha||3.895s|
|11||Cal Crutchlow||LCR Honda||Honda||4.370s|
|12||Franco Morbidelli||Petronas Yamaha||Yamaha||6.651s|
|13||Takaaki Nakagami||LCR Honda||Honda||2.512s|
|14||Francesco Bagnaia||Pramac Ducati||Ducati||2.533s|
|16||Miguel Oliveira||Tech3 KTM||KTM||3.010s|
|20||Karel Abraham||Avintia Ducati||Ducati||4.145s|
|21||Hafizh Syahrin||Tech3 KTM||KTM||4.402s|
|22||Tito Rabat||Avintia Ducati||Ducati||4.562s|