What was forecast to be the best day of the weather-disrupted test ultimately delivered another rain-hit morning before the track dried towards the end of the afternoon.
Crutchlow judged the drying circuit best and set a 1:9.511s on his Tech 3 Yamaha, edging out factory rider and Sunday pacesetter Valentino Rossi by 0.244 seconds.
Stefan Bradl enjoyed his best performance of the winter as he got his LCR Honda up to third, demoting champion Jorge Lorenzo and denying Yamaha a top-three sweep.
Marc Marquez was fifth and the sole works Honda rider in action.
Troubled by the neck pain that has afflicted him at times in recent weeks and feeling he had nothing more to learn in the wet, Dani Pedrosa decided to head home early.
Pramac's Ben Spies did not run either, while Alvaro Bautista sat the session out to rest the knee and finger injuries he sustained in his Sunday crash.
Top Ducati rider Andrea Iannone was within 0.8s of the pace in sixth, followed by works men Nicky Hayden and Andrea Dovizioso, who had warned on Sunday not to take the bike's apparent improvement too seriously given the weather.
Randy de Puniet returned to the head of the CRT pack in 10th for Aspar, pushing Crutchlow's team-mate Bradley Smith outside the top 10. But the young Briton had led the way for a while when the track began to dry.
Ducati test rider Michele Pirro was quickest of the few riders who took part in the morning's wet running.
1. Cal Crutchlow Tech 3 Yamaha 1:39.511s
2. Valentino Rossi Yamaha 1:39.735s + 0.224s
3. Stefan Bradl LCR Honda 1:39.975s + 0.464s
4. Jorge Lorenzo Yamaha 1:40.105s + 0.594s
5. Marc Marquez Honda 1:40.130s + 0.619s
6. Andrea Iannone Pramac Ducati 1:40.331s + 0.820s
7. Nicky Hayden Ducati 1:40.370s + 0.859s
8. Andrea Dovizioso Ducati 1:40.516s + 1.005s
9. Michele Pirro Ducati 1:40.881s + 1.370s
10. Randy de Puniet Aspar Aprilia 1:40.971s + 1.460s