Simoncelli was killed at Sepang after losing control of his Gresini Honda and being hit by Colin Edwards and Valentino Rossi, and the field of riders all carried various tributes to the Italian at the Circuit Ricardo Tormo, with many carrying his racing number 58 on their leathers and helmets.
As so often this season it was Stoner who led the way upon his Repsol Honda, with his fastest time of one minute 45.513 seconds from a damp morning session being enough to top the timesheets as heavier rain ensured slower times during the afternoon.
The Australian headed team-mate Dani Pedrosa by 0.2 seconds while the damp conditions provided Ducati with a positive day after a difficult season with the problematic GP11.
Rossi and team-mate Nicky Hayden secured the third and fourth fastest times while Loris Capirossi, who will retire after making his 215th Grand Prix start at this weekend's season finale, was fifth on the customer Pramac Ducati.
Ben Spies was the top Yamaha rider in sixth place with Randy de Puniet and Tony Elias next up.
Andrea Dovizioso began his last weekend with Repsol Honda with ninth place, while the Italian's future team-mate, Britain's Cal Crutchlow, rounded out the top 10.
Hiroshi Aoyama, the sole Gresini rider in Simoncelli's absence, ended the day 14th of the 16 riders.
Suzuki's Alvaro Bautista topped the times in the wet second session, but was 11th overall.
Despite being quickest, Stoner said that the day's running had been "useless" due to the constantly changing weather conditions, and hopes the grip available on track will be more consistent ahead of Saturday's qualifying.
"It hasn't been a great day to be honest, we've never had a great feeling here in the wet," he said.
"I love riding this circuit in the dry, but there seems to be some sort of oil or grease on the circuit, I'm not sure if it's due to a lot of car rubber down but it makes things hard for sure.
"It's been pretty useless in terms of finding a good set up, both sessions began with a little water and then drying out towards the end, when it's like this you're chasing the set up all day so we didn't do too much work on the bike.
"We tried a few small things to make it better in the wet, but then as it dried up we saw everything we had done was a waste of time. We'll wait and see what tomorrow brings and if it does rain again I hope it at least rains consistently so we can get a full wet session in."
Fausto Gresini, meanwhile, spoke of the difficulties his team had faced in returning to racing so soon after the death of lead rider Simoncelli, but praised Aoyama's efforts in challenging circumstances.
"There is so much sadness in our garage today," he said.
"The atmosphere was surreal without 'Super Sic' there and it has been extremely difficult to tackle the day. It goes without saying that he is missed but it was important for us to be here and honour his memory because I am sure this is what he would want.
"Hiroshi tried to find the limit in difficult conditions but it was tough for him. I am sure he will give his best on Sunday in Marco's name."