Yamaha’s satellite SRT riders Franco Morbidelli and Fabio Quartararo took the honours in the afternoon session, but could not better Marquez’s effort in cooler conditions in the morning.
Track temperatures soared to 54 degrees Celsius for the second session, with similar blistering conditions forecast for Sunday’s Spanish MotoGP in Andalusia.
Marquez, and his younger brother Alex, who has joined him at Honda for the season, both came off their bikes in second practice, but both were quickly back on board, unscathed.
Quartararo’s promising performance came after the Frenchman was forced to sit out 20 minutes of the first session because of a penalty.
Third in second practice came Brad Binder, the south African MotoGP rookie on a KTM.
The 2020 MotoGP world championship finally gets underway on Sunday, behind closed doors and more than four months late, with Spaniard Marquez going for a seventh top-class title to match Valentino Rossi.
Jerez in Spain hosts the first two races a week apart. The championship will then move to the Czech Republic for one race, and then to Austria for the next two, probably still without spectators.
Saturday sees a third practice session before qualifying.
Combined first and second practice times at Jerez
1. Marc Marquez (ESP/Honda) 1min 37.350sec, 2. Maverick Vinales (ESP/Yamaha) at 0.024s, 3. Cal Crutchlow (GBR/Honda-LCR) 0.088, 4. Andrea Dovizioso (ITA/Ducati) 0.121, 5. Joan Mir (ESP/Suzuki) 0.131, 6. Jack Miller (AUS/Ducati-Pramac) 0.137, 7. Alex Rins (ESP/Suzuki) 0.219, 8. Pol Espargaro (ESP/KTM) 0.362, 9. Iker Lecuona (ESP/KTM-Tech3) 0.364, 10. Brad Binder (RSA/KTM) 0.573, 11. Johann Zarco (FRA/Ducati-Avintia) 0.590, 15. Fabio Quartararo (FRA/Yamaha-SRT) 0.802