The arrival of rain with a little under 20 minutes to go meant it was the top 10 riders from Friday who secured the automatic Q2 spots, with Maverick Vinales' best time of 1m39.477s remaining unbeaten.
That means the likes of Dani Pedrosa, Andrea Dovizioso, Valentino Rossi and Jorge Lorenzo will contest first phase of qualifying, in which the final two places in Q2 are up for grabs.
Crutchlow was the only man in the top 10 to improve from Friday on Saturday morning, posting a 1m39.722s to lead the session by 0.115 seconds from Vinales.
The British rider moved from seventh to second in the combined practice order on the strength of that time, ahead of Honda's Marc Marquez and Aspar Ducati pair Karel Abraham and Alvaro Bautista.
"It's now raining quite a lot," Crutchlow said when running had effectively finished.
"The problem was, there were no rain flags. Sure, we could see on the screen, and the visor and it's more of that rain that you can push.
"You are able to continue to push a little bit, but you're not going to better your own lap times and you're not really learn much."
Danilo Petrucci (Pramac Ducati), Loris Baz (Avintia Ducati), Jonas Folger (Tech3 Yamaha), Aleix Espargaro (Aprilia) and Andrea Iannone (Suzuki) sealed the remaining Q2 places.
Pedrosa was third-fastest in the session with a 1m40.292s, moving up to 11th overall, but missed out on a free pass to Q2 by a scant 0.042s.
The second Pramac Ducati of Scott Redding, Marquez and Baz completed the top six on Saturday morning, followed by Marc VDS Honda's Jack Miller and Dovizioso on the best of the factory Ducatis.
Dovizioso failed to improve on his Friday time, and stayed 14th in the combined order, four places clear of team-mate Lorenzo, who was only 14th-fastest in the session.
Rossi was another rider unable to better his previous best, the Yamaha rider slipping to 17th in the combined order behind Miller, with the 12-best time in third practice.
Pol Espargaro, who was one of a handful riders to try a full wet track in the closing minutes, was best of the KTM runners in 21st overall, 1.873s off the pace.
EXTRA FRONT TYRE DISCARDED
Following feedback from a handful of riders led by Valentino Rossi, Michelin brought a soft front tyre with a stiffer construction - as used at Valencia last year - to Argentina.
However a transport strike meant the tyres only arrived at the circuit on Friday evening, and in their regular Safety Commission meeting after practice, riders agreed to not use the option tyre this weekend.
PRACTICE THREE TIMES:
Read the original article on Eurosport: Crutchlow tops rain-hit third practice