Tech 3's Bradley Smith timed his final run to perfection as he set the fastest time on a drying track at Estoril.
Sunday morning saw the Portuguese circuit bathed in sunshine but overnight rain had left the track unsuitable for slick tyres. With conditions steadily improving the final laps were going to make the difference, and the Oxford rider proved that with a 1:53.622s to knock Andrea Iannone off the top.
Wet weather specialist Anthony West was never far from the top of the timesheets and the Australian was 0.150s slower than Smith in second.
Scott Redding completed a promising morning for the Brits in third while championship leader Iannone dropped back to fourth. Marc Marquez was fifth with front row qualifiers Julian Simon and Thomas Luthi were sixth and seventh.
Xavier Simeon was eighth, continuing the form that saw him achieve his strongest qualifying result of the season yesterday. The Belgian fulfilled his promise that the Mistral 610 was working to his liking in any condition.
Pole sitter Stefan Bradl stayed out of trouble to take twelfth and will be hoping for a dry race after fading in wet conditions at Jerez last time out.
Kev Coghlan opted not to go out at all as the Scotsman looks to nurse the injuries he brought into the weekend. With conditions so changeable, the Aeroport de Castello rider took the safe option.
That might have been a wise decision for Kenny Noyes who crashed out at the beginning of the session. South African Steven Odendaal also slid off the track but both were uninjured and will line up for the race at 11:15 BST.