Stoner and his Honda team mate Dani Pedrosa took the top two positions on the time sheets for Thursday's (March 1) MotoGP test at Sepang.
Honda sat out Wednesday's (February 29) test while an engine problem was investigated, but all four Hondas were on the track in good, dry conditions for the final day of testing in Malaysia on Thursday.
Stoner set a time of two minutes 0.473 seconds with Pedrosa 0.175 seconds behind. Third was Andrea Dovizioso on a Tech3 Yamaha ahead of the first of the factory Yamahas - ridden by 2010 world champion Jorge Lorenzo. Lorenzo's team mate Ben Spies was down in eighth place.
Fifth was Cal Crutchlow on the second of the Tech3 Yamahas.
At the end of the day Casey Stoner summed up his team's work at Sepang, and their remaining problem with "chatter"
"It's been good to get some good weather and get out there and find some different solutions with the bike," he said.
"We've been trying a few different things with the electronics, just with fuel consumption, just trying to reduce the fuel consumption while trying to keep the engine profile the same as what we want. So I've been working on that today quite a lot. We've tried a couple of other things with the chassis, tried to shorten it to try to get rid of the chattering.
Unfortunately whatever we are able to do, we are able to reduce the chattering a little bit but we can't really get it to disappear so we've got quite a lot of work to do. We've still to cover that sort of problem but in general the chassis balance here is good, the traction of the bike feels good, it's turning quite well and everything but we have really got to get rid of that chatter to get a good understanding of it."
Out of the top five came a Ducati but it was the Pramac Racing machine of Hector Barbera rather than the factory Ducatis.
Seventh was Alvaro Bautista on the Honda Gresini machine and Moto2 graduate Stefan Bradl on the LCR Honda ninth.
Then came former world champions Valentino Rossi and Nicky Hayden who are riding the official factory Ducatis. They were down in 10th and 11th places and disappointed that the new bikes are not up with the Hondas or Yamahas.
The final test comes at Jerez in Spain, starting on March 23 before the first Grand Prix - the night race at Qatar's Losail circuit on April 8.
MotoGP test times according to Dorna Sports SL
1 Casey Stoner Repsol Honda Team 2:00.473 34 laps
2 Dani Pedrosa Repsol Honda Team 2:00.648 +0.175
3 Andrea Dovizioso Monster Yamaha Tech 3 2:00.802 +0.329
4 Jorge Lorenzo Yamaha Factory Racing 2:00.877 +0.404
5 Cal Crutchlow Monster Yamaha Tech 3 2:00.986 +0.513
6 Hector Barbera Pramac Racing Team 2:01.231
7 Alvaro Bautista Honda Gresini 2:01.275
8 Ben Spies Yamaha Factory Racing 2:01.432
9 Stefan Bradl LCR Honda 2:01.492
10 Valentino Rossi Ducati Team 2:01.550
11 Nicky Hayden Ducati Team 2:01.609
12 Franco Battaini Cardion AB Motoracing 2:03.490
13 Colin Edwards NGM Mobile Forward Racing 2:03.681
14 Yonny Hernandez Avintia Racing 2:06.632
15 Ivan Silva Avintia Racing 2:06.785
source: newshub archive