Ferrari were the Silver Arrows’ closest challengers, but Sebastian Vettel and Kimi Raikkonen were over a second off the pace in third and fourth, with the Red Bulls of Daniel Ricciardo and Max Verstappen - who opted not to use the yellow-marked soft tyre - several tenths further back.
The top ten was completed by the Force Indias of Nico Hulkenberg and Sergio Perez, the McLaren of Fernando Alonso – who suffered an early off at Spoon Curve – and the Williams of Valtteri Bottas.
Alonso wasn’t the only driver to test the Suzuka barriers – Romain Grosjean also went off, nosing his Haas in the tyres at Degner after a big lock-up.
Mercedes stayed out of the walls, but it wasn't all plain sailing - Hamilton complained about 'low power' early on, while Rosberg suffered with 'monster understeer' and later reported some engine cuts.
Red Bull too had complaints - Verstappen said the upshifts on his RB12 were "like a handbrake" early on, while both he and Ricciardo struggled with the handling of the RB12 as they focused on hard and medium tyre runs. Even so, the pair wound up fifth and sixth - Ricciardo had the upper hand by the measure of a few tenths of a second.
Verstappen was the last man to get within 2s of Rosberg's benchmark - Hulkenberg in seventh was 2.099s down, with Perez a few tenths down the road. Alonso was a similar gap behind the Mexican, although like Red Bull he too opted not to use the softs.
Valtteri Bottas locked out 10th for Williams and was the morning's busiest driver with 31 laps on the board. At the other end of the scale, Renault's Jolyon Palmer was limited to 13 as electrical problems brought his morning to a slightly early halt.
WATCH: Early spin puts Alonso into the barriers
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