Sylvain Guintoli was leading the Assen World Superbike first qualifying timesheets when rain arrived, preventing any threat to the Frenchman's position.
The Effenbert Liberty star - who took a podium in the first race of the year but has slipped to ninth in the standings after scoring points just once since - finished the session with a slim advantage of 0.030s over Kawasaki's Tom Sykes.
Sykes set his best time moments after Guintoli, who had taken provisional pole from Crescent Suzuki's Leon Camier just three-minutes into the qualifying session. Camier's time kept him in third place, albeit 0.868s from Guintoli.
Reigning champion and 2012 title leader Carlos Checa was credited with fourth place for Althea Ducati, just over one-second from the top.
The Althea Ducati rider and fifth placed Jonathan Rea (Honda World Superbike) were among those to try some wet laps, which could prove useful with variable weather a threat for the remainder of the weekend. Rea and Checa shared race wins at Assen last year.
The BMW trio of Michel Fabrizio, Aryton Badovini and morning pace setter Marco Melandri filled places six to eight. Melandri completed the most laps this afternoon, with eleven, and his morning time beat Guintoli's qualifying best by 0.018s.
The Italian was followed on the timesheets by Guintoli's team-mate Maxime Berger, with ParkinGO Aprilia's Chaz Davies an improved tenth from 21st in practice. Davies was also the top RSV4 rider in qualifying, despite completing just two flying laps, with factory star Eugene Laverty eleventh.
Aprilia's former world champion and 2012 race winner Max Biaggi will be among those hoping the weather improves for second qualifying, having been just 17th in both of Friday's sessions - and thus presently out of Superpole. Biaggi completed just two laps this afternoon.
Melandri's team-mate Leon Haslam was also caught out by the weather, registering 14th in qualifying, having been sixth quickest this morning.