With Laguna the only MotoGP venue that feeder categories Moto2 and Moto3 do not visit, Marquez had not tried the venue until Friday practice.
But that did not stop him taking third in the morning, and in practice two he took control halfway through the session.
The factory Honda rider ended up on a 1m22.040s, 0.229 seconds ahead of nearest rival Stefan Bradl on the LCR Honda.
Just 0.077s covered Bradl, Ducati's Andrea Dovizioso and Valentino Rossi's Yamaha in second to fourth places.
Morning pacesetter Cal Crutchlow was back in fifth this time.
The still-recovering Jorge Lorenzo and Dani Pedrosa both completed over 20 laps.
But while Lorenzo got up to sixth place, 0.4s off the pace and within 0.010s of Crutchlow, Pedrosa was back in 11th position, a second adrift.
Aleix Espargaro remained on top in CRT in seventh overall, ahead of Alvaro Bautista, Nicky Hayden and Bradley Smith's prototype bikes.
The session was delayed by 20 minutes when American wildcard Blake Young had a huge high-side at Turn 5.
While Young walked away from the violent tumble, his APR-Kawasaki bounced destructively down the track, dropping fluid in the process and forcing the long stoppage.
- Sports & Recreation
- Dani Pedrosa
- Stefan Bradl
- Jorge Lorenzo
- Andrea Dovizioso