The Spaniard was unable to better his time from the morning session in the hot track conditions in the afternoon, but his FP1 best time of 1m 39.300s was enough to give him a 0.128s advantage over Marquez, who was eighth fastest in the morning.
Marquez, who is riding this week with a finger injury after a dirt bike accident last weekend, set his fastest time with eight minutes to go in the session, edging out Ducati's Andrea Iannone – who set the pace earlier in the session with his in 1m 39.51s – into third place.
His team-mate Andrea Dovizioso made use of the soft tyre late in the session to finish in fourth place, just 0.024s behind his Italian team-mate.
The top six was rounded out by Suzuki's Aleix Espargaro and Pramac Ducati's Danilo Petrucci.
Cal Crutchlow on the CWM LCR Honda was third fastest in the morning but dropped down to seventh place – the Briton's best lap was a 1m 39.909s some 0.609s off Lorenzo's morning pace.
Pol Espargaro on the Monster Yamaha Tech 3 bike was eighth, followed by rookie Maverick Vinales (Suzuki) and Scott Redding on the Estrella Galicia in 10th.
Redding's best time was 0.845s slower than that leading time.
Championship leader Valentino Rossi was sixth fastest in FP1 but dropped down to 13th in the afternoon session.
The veteran champion ended up behind Bradley Smith (Monster Yamaha Tech 3) in 11th and Yonny Hernandez (Pramac Racing) on the time sheets.
The top 15 was completed by Mike de Meglio on the Avintia Ducati and Eugene Laverty on the Power Electronics Aspar Honda, although the Ulsterman's time of 1m 40.514s on the Open class machine was more than 1.2s adrift of first place.
Complete FP2 times:
1. Jorge Lorenzo ESP Movistar Yamaha MotoGP (YZR-M1) 1m 39.300s [Lap 14/20] 291km/h (Top Speed)
2. Marc Marquez ESP Repsol Honda Team (RC213V) 1m 39.428s 0.128s [4/16] 293km/h
3. Andrea Iannone ITA Ducati Team (Desmosedici GP15) 1m 39.511s 0.211s [18/18] 292km/h
4. Andrea Dovizioso ITA Ducati Team (Desmosedici GP15) 1m 39.535s 0.235s [17/17] 293km/h
5. Aleix Espargaro ESP Team Suzuki Ecstar (GSX-RR) 1m 39.616s 0.316s [8/18] 282km/h
6. Danilo Petrucci ITA Pramac Racing (Desmosedici GP14.1) 1m 39.718s 0.418s [2/18] 290km/h
7. Cal Crutchlow GBR CWM LCR Honda (RC213V) 1m 39.909s 0.609s [14/18] 290km/h
8. Pol Espargaro ESP Monster Yamaha Tech 3 (YZR-M1) 1m 39.953s 0.653s [13/15] 291km/h
9. Maverick Vinales ESP Team Suzuki Ecstar (GSX-RR) 1m 40.087s 0.787s [15/18] 284km/h
10. Scott Redding GBR Estrella Galicia 0,0 Marc VDS (RC213V) 1m 40.145s 0.845s [16/17] 292km/h
11. Bradley Smith GBR Monster Yamaha Tech 3 (YZR-M1) 1m 40.293s 0.993s [17/20] 289km/h
12. Yonny Hernandez COL Pramac Racing (Desmosedici GP14.2) 1m 40.363s 1.063s [14/15] 293km/h
13. Valentino Rossi ITA Movistar Yamaha MotoGP (YZR-M1) 1m 40.394s 1.094s [9/19] 289km/h
14. Mike Di Meglio FRA Avintia Racing (Desmosedici GP14 Open) 1m 40.444s 1.144s [15/19] 289km/h
15. Eugene Laverty IRL Aspar MotoGP Team (RC213V-RS)* 1m 40.514s 1.214s [12/18] 283km/h
16. Hector Barbera ESP Avintia Racing (Desmosedici GP14 Open) 1m 40.569s 1.269s [2/18] 291km/h
17. Hiroshi Aoyama JPN Repsol Honda Team (RC213V) 1m 40.678s 1.378s [16/18] 292km/h
18. Alvaro Bautista ESP Factory Aprilia Gresini (RS-GP) 1m 40.752s 1.452s [19/19] 281km/h
19. Nicky Hayden USA Aspar MotoGP Team (RC213V-RS) 1m 40.819s 1.519s [15/18] 279km/h
20. Stefan Bradl GER Athina Forward Racing (Forward Yamaha) 1m 40.825s 1.525s [11/13] 286km/h
21. Karel Abraham CZE Cardion AB Motoracing (RC213V-RS) 1m 40.917s 1.617s [13/15] 284km/h
22. Jack Miller AUS CWM LCR Honda (RC213V-RS) 1m 41.226s 1.926s [13/16] 284km/h
23. Loris Baz FRA Athina Forward Racing (Forward Yamaha)* 1m 41.422s 2.122s [3/18] 281km/h
24. Marco Melandri ITA Factory Aprilia Gresini (RS-GP) 1m 41.450s 2.150s [15/16] 283km/h
25. Alex De Angelis RSM Octo IodaRacing (ART) 1m 42.176s 2.876s [9/14] 277km/h
Top 10 Combined Practice Times after FP2:
1. Jorge Lorenzo ESP Movistar Yamaha MotoGP (YZR-M1)
2. Aleix Espargaro ESP Team Suzuki Ecstar (GSX-RR)
3. Marc Marquez ESP Repsol Honda Team (RC213V)
4. Andrea Iannone ITA Ducati Team (Desmosedici GP15)
5. Andrea Dovizioso ITA Ducati Team (Desmosedici GP15)
6. Danilo Petrucci ITA Pramac Racing (Desmosedici GP14.1)
7. Cal Crutchlow GBR CWM LCR Honda (RC213V)
8. Pol Espargaro ESP Monster Yamaha Tech 3 (YZR-M1)
9. Valentino Rossi ITA Movistar Yamaha MotoGP (YZR-M1)
10. Maverick Vinales ESP Team Suzuki Ecstar (GSX-RR)