Marquez claimed his eighth pole position of the season on his last timed lap and will line up on the front now next to a pair of Yamaha riders.
Both Ducati Team riders hope to reduce their gaps to the leaders.
Dani Pedrosa’s time was just two-tenths of a second off the qualifying lap record, the Spaniard topping the opening day ahead of teammate Marc Marquez.
There are still some small changes to be made to the Desmosedici GP13 to increase Yonny Hernandez's confidence for qualifying tomorrow.
Andrea Iannone concluded this first day of the challenging Malaysian Grand Prix in 12th position.
Cal Crutchlow setting the third fastest time on the opening day of practice at the physically demanding Sepang International Circuit.
Repsol Honda pair quickly up to speed with Crutchlow third fastest
Nine-time world champion Valentino Rossi made solid improvements over the two practice sessions to wrap up the day in fourth in the combined times.
Rossi and Lorenzo both like the Sepang Circuit a lot, but the heat not so much.
Repsol Honda teammates will have to explain race incident at Aragon
Jorge Lorenzo and Valentino Rossi completed the test days in Malaysia with changes to the original programme. Lorenzo leaves with the fastest overall best laptime.
Rain in the morning made it impossible to follow the regular testing program, but fortunately the conditions were back to normal for the afternoon.
Bradley Smith did not let the rain deter his positive learning curve on the Yamaha YZR-M1 as both the newcomer to the Tech 3 team, and returnee rider Cal Crutchlow leave Malaysia on a high note.
The Pramac teams will be had to Jerez for their final test before the first grand prix.
Yamaha factory rider Jorge Lorenzo set the benchmark for the other riders to aim for.
Rookie rider Marc Márquez challenging at the front after Malaysia test while his team mate Dani Pedrosa sets his eyes on 2013 crown.
Factory Hondas edge out Yamaha on final day of second MotoGP test of 2013
Cal Crutchlow stormed to the second best lap in MotoGP second day of testing at Sepang on his Monster Yamaha Tech 3 Team YZR-M1.
Repsol Honda rider Dani Pedrosa targets long run on Wednesday in testing at Sepang, Malaysia,
The Monster Y amaha Tech 3 Team riders both finished inside the top 10 on a rain-hit first day.
Yamaha Factory Team was back in Malaysia for the second round of testing at the Sepang International Circuit and day one was hampered by the weather.
Extreme weather at the Sepang circuit did not make for a pleasant day for the Ducati team in Malaysia.
Repsol Honda rider leads the way on day one in Malaysia
Ducati team kicked off the new season with the RTA-organized test at the Malaysian Sepang circuit.
The first testing for the MotoGP teams ended on a high note for Repsol Honda in Sepang, Malaysia,
Spaniard tops all three days of testing and sets time under current lap record
The Repsol Honda Team has begun 2013 in the best possible way, with Dani Pedrosa and Marc Marquez finishing the first day first and third respectively.
Pace set by Pedrosa on opening day of first official MotoGP test
Crutchlow and Smith kick off 2013 preparations in Sepang testing