Marquez was the first rider to try slick tyres in the closing minutes.
The lap seemed to be going well until the approach to the very fast Ramshoek, just after the point where Jorge Lorenzo broke his collarbone on Thursday.
Marquez appeared to hit a damp patch and was thrown into a violent high-side, landing on his shoulders and then being collected by his sliding Honda before tumbling through the gravel.
Despite the ferocity of the crash, Marquez walked away unaided and was confirmed to be shaken but unhurt.
Meanwhile, off-track suggestions that Lorenzo would still attempt to race on Saturday swirled around the paddock, with Yamaha declining to rule the possibility out.
Lorenzo had successful surgery in Barcelona overnight, and is guaranteed a top-12 start if he is passed fit as his practice one time on a dry track held up as the fastest of the weekend so far, getting him into Q2.
On the circuit, Bautista eventually got down to the fastest wet time for Gresini Honda, then made successful use of slicks to set a 1m40.029s as the chequered flag came out.
That lap denied Aspar's Randy de Puniet the chance to top the session on his CRT Aprilia, the Frenchman ending up 0.194 seconds slower.
Two stand-ins were next up: Ben Spies' Pramac substitute Michele Pirro was third on the 'lab' Ducati in an unusual top 10, followed by Avintia's returnee Ivan Silva, deputising for Hiroshi Aoyama.
Marquez was classified fifth with his best wet-tyre time.
Works Ducati riders Nicky Hayden and Andrea Dovizioso plus Pramac man Andrea Iannone will all have to get through Q1 in qualifying as they were outside the top 10 in the weekend's sole dry practice session so far.
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