Under bright sunshine on a dry track, albeit one that was slow to grip up, the Woking team dominated proceedings in the first 90 minutes. Only Red Bull's Mark Webber looked anywhere near close to the two British drivers in terms of pace.
Webber ended the morning session third fastest, ahead of the two Mercedes of Nico Rosberg and Michael Schumacher - embarking on his final grand prix at Suzuka.
Rosberg's W03 actually ground to halt out of Turn 4 in the final minutes of the session which effectively brought running to a premature end.
Kamui Kobayashi, who had predicted impressive performance from Sauber this weekend, was sixth fastest on the resurfaced lay-out (new asphalt is down between Turn 7 and the chicane) ahead of Ferrari's Felipe Massa and Paul di Resta in the Force India.
Nico Hulkenberg and Pastor Maldonado completed the top ten.
The McLarens looked fast from the outset, or at least as soon as cars started posting serious laptimes, which was from about half an hour in.
Hamilton was the first to go top with a 1m37.008s lap, and it was a while before anyone got close to that, partly it seemed due to the apparent low grip conditions.
Indeed several cars had lairy moments, not least Schumacher who ran wide at Degner and Grosjean who had a similar escapade at Spoon.
Halfway through the session and Webber, on the hard tyre, moved to the front in the Red Bull with a 1m34.740s. That after his own scary DRS-open moment through 130R.
The Australian remained fastest until the turn of the hour when Button, last of the front-runners to put in a proper run, set his 1m34.507s. Shortly after that Hamilton re-emerged from the pits to go 0.233s slower, making it a McLaren one-two ahead of Webber.
With most drivers then staying on the worn hard primes for their second runs, there was little further activity on the timesheets short of Schumacher's improvement to fifth.
Kimi Raikkonen was 13th in the fastest Lotus, two places behind world championship leader Fernando Alonso, while the reigning champion Sebastian Vettel was 17th. The the wry smile from the German as he removed his helmet post session suggested he was unconcerned that he was nearly 2s off the pace though.