The Ducati rider clocked a best lap of one minute 45.140 seconds at Motegi, dominating the second session with Jorge Lorenzo (+0.440secs) his closest rival.
Yamaha's Lorenzo fared better than team-mate Valentino Rossi (+0.750secs), while Repsol Honda's Marquez was sixth in second practice, 0.799secs slower than Dovizioso.
Stefan Bradl for LCR Honda (+0.497secs) and Repsol Honda's Dani Pedrosa (+0.587secs) were also quicker than the runaway championship leader, placing third and fourth respectively.
Also within a second of Dovizioso were Monster Yamaha Tech 3 pair Pol Espargaro (+0.901secs) and Bradley Smith (+0.965secs), and Pramac Racing's Andrea Iannone (+0.967secs).
Earlier, Lorenzo topped first practice in a time of 1:45.838secs, ahead of Marquez (+0.166secs) and Dovizioso (+0.234secs).
Marquez can seal a second consecutive MotoGP title with victory in Sunday's race, with a further three grands prix to come before the end of the season.