With Casey Stoner having wrapped up the title last week, the team were in buoyant mood and Dani Pedrosa led the way for them on Friday, scorching to a best lap of two minutes 01.250 seconds.
He was a full eight tenths ahead of Stoner, with Andrea Dovizioso nearly one and a half seconds behind his pacesetting team-mate.
Another Honda rider, Marco Simoncelli, was fourth, with Hiroshi Aoyama fifth, one tenth behind Simoncelli's two minutes 02.832 secs.
Colin Edwards was the quickest non-Honda rider, sixth fastest on his Yamaha, with Suzuki's Alvaro Bautista seventh.
Randy de Puniet (Ducati) was next, although a full two seconds slower than Pedrosa, with Ben Spies in ninth.
The top 10 was made up by Karel Abraham (Cardion AB Motoracing), with Nicky Hayden 11th on his Ducati and his team-mate Valentino Rossi further back in 13th.
With Jorge Lorenzo missing after hand surgery, Yamaha replacement Katsuyuki Nakasuga ended 18th, having crashed twice following a promising start.