In a reverse of Friday morning’s FP1 session, Marquez led Martin by 0.174 seconds after posting a 1m57.823s on his final flying lap.
KTM duo Jack Miller and Brad Binder trailed the Ducati pair, while Maverick Vinales was fifth on his factory Aprilia as team-mate Aleix Espargaro crashed three times.
Championship leader Francesco Bagnaia was eighth and secured a place directly into Q2 for Saturday’s qualifying.
The hour-long second practice session took place under grey skies at the Sepang International Circuit, but the rain stayed away.
Marc Marquez set the early pace on his factory Honda at 1m59.515s before younger brother Alex edged ahead with a 1m58.705s just over five minutes in.
This would stay as the reference lap for a while, before Martin posted a 1m58.523s with around 38 minutes to go.
With just under 15 minutes to run, Bagnaia took over from Martin with a 1m58.493s, only to be immediately deposed by Yamaha’s Fabio Quartararo.
Quartararo’s 1m58.399s didn’t keep him top for long, as KTM’s Binder edged ahead with a 1m58.310s before Martin fired in a 1m58.227s with just under 11 minutes to go to return to top spot.
Source: Autosport