Danilo Petrucci topped the FP2 session in Valencia in extremely wet conditions with a 1.41.318 on the Alma Pramac Ducati.
Marc Marquez finished the session in second place, +0.407 behind the fastest time on the Repsol Honda and Valentino Rossi finished in third on the Movistar Yamaha.
Difficult conditions continued for the MotoGP riders as heavy rain lashed down onto the circuit. The session was red flagged due to track conditions, just like FP1, with 36 minutes remaining.
Andrea Iannone finished in fourth place with Aleix Espargaro on the Aprilia in fifth place and brother Pol Espargaro in sixth place on the KTM.
The second factory Yamaha of Maverick Vinales finished in seventh place.
Scott Redding finished in eighth place alongside fellow Brit Bradley Smith in ninth on the KTM.
Alex Rins rounds out the top ten on the Suzuki.
Xavier Simeon finished 11th and ahead of factory Ducati rider Andrea Dovizioso in 12th.
Jorge Lorenzo finished the session in P15.
Johann Zarco crashed just before the red flag came out but ended the session in P19.
Ducati test rider Michele Pirro finished the session down in 21st place.
Dani Pedrosa at his last MotoGP race finished the session in P24.