With track temperatures 20C cooler than on Friday afternoon, five riders crashed inside the first 15 minutes, all losing the front end in windy conditions.
Riders reported the track surface lacked grip and felt like it had moisture in it, with it already significantly bumpier than last year.
Suzuki rookie Alex Rins was the first to come unstuck, at Turn 19 on his first timed lap, and will take no further part in the weekend after fracturing his left wrist.
Turn 2 accounted for Aspar Ducati's Alvaro Bautista and factory Ducati rider Andrea Dovizioso, their spills split by Aleix Espargaro crashing at Turn 13, right in front of Valentino Rossi.
Espargaro's Aprilia team-mate Sam Lowes then crashed at Turn 2, in a carbon copy of Bautista and Dovizioso's accidents.
The middle of the session was calmer, before Marquez, Andrea Iannone on the other Suzuki and Espargaro - for a second time - fell at Turns 18, 19 and 14 within the space of two minutes, entering the final 20 minutes.
The slippery conditions meant lap times did not come close to the pace set during practice on Friday afternoon until the last five minutes, and only seven riders improved on their best laps.
Marquez set a 2m04.687s inside the first 10 minutes, and that stood as the fastest time of Saturday morning until he crashed for a second time with five minutes remaining, highsiding applying power at Turn 15 on an outlap.
LCR Honda's Cal Crutchlow then moved into top spot with a lap of 2m04.677s, before Yamaha's Vinales took control.
The championship leader logged a 2m04.241s, and followed that up with the weekend's first sub-2m04s lap, a 2m03.979s inside the final minute.
That time was 0.082 seconds quicker than Marquez's Friday benchmark, and 0.317s up on Dani Pedrosa in second place in this session, while Crutchlow was third, 0.698s adrift.
Marquez wound up fourth, ahead of satellite riders Scott Redding, Jack Miller, Johann Zarco, Loris Baz, Tito Rabat and Danilo Petrucci.
However the same 10 riders that occupied the guaranteed Q2 places at the end of Friday's running will still progress straight to that session, albeit with some minor changes to the order now led by Vinales.
He will be joined in Q2 by Marquez, Pedrosa, Zarco, Crutchlow, Rossi - 15th in third practice - Dovizioso, Redding, Folger and Iannone.
Miller's lap to be sixth on Saturday morning for Marc VDS Honda could not displace Iannone for the final Q2 spot, while Lorenzo will also contest the first phase of qualifying for the second time in as many races.
The Ducati recruit crashed at Turn 19 in the closing stages of the session, and was 12th in both the third-practice and combined-practice orders.
Read the original article on Eurosport: Vinales leads FP3 as Marquez and Lorenzo fall