With world champion Lewis Hamilton at the wheel as the Portimao asphalt dried out, McLaren re-fitted the 2009-specification rear wing to the MP4-24, but it was Nico Rosberg who set the new-carpace in Williams' newly launched FW31.
The German amassed a massive 143 laps to be less than two seconds slower than the fully 2008-spec Toro Rosso of Sebastien Buemi.
Hamilton, suffering from a common cold, trailed a few tenths behind Rosberg, followed by Timo Glock's Toyota TF109 and finally the new Renault driven by Fernando Alonso.
Glock had the most noteworthy technical failure after a broken oil pipe caused a fire at the rear of the car, but Hamilton also stopped out on track with what the team described as an "engine systems shutdown".
More rain is forecast for the final day of the test on Thursday.
Ferrari's decision to move its running from Portimao to Mugello, meanwhile, was looking shaky on Wednesday, as Felipe Massa took over from Kimi Raikkonen for a third consecutive day of wet running with the F60.
The conditions never allowed slick tires to be fitted, but the Brazilian at least managed more than 100 laps of the Italian venue.
Raikkonen, who left the circuit on Tuesday evening, defended the team's decision to abandon Portugal ostensibly because of the weather forecast.
"I think it's raining over there too," he told La Gazzetta dello Sport. "At least here we're close to home and it's easier to send people back and forth when needed."
It was sunny at Valencia in Spain, where BMW-Sauber has exclusive use of the Ricardo Tormo circuit for the new F1.09's first test.
In windy conditions, Robert Kubica completed nearly a century of laps ahead of three more days of testing for the Hinwil based team.