A 2:18.397s best from Martin aboard the #45 Marc VDS BMW proved 0.009s quicker than Vanthoor's #1 WRT Audi in the afternoon's first qualifying session.
The #45 entry, which Martin shares with Dirk Werner and Augusto Farfus, remained on top after the night session, which was topped by the #2 WRT Audi.
The combined result set the order for Friday's top 20 Superpole shootout, while locking in 21st through 57th on the packed grid for the showpiece GT3 event.
The team's progress had been slowed earlier in the day, missing the end of Practice 1 after Estre made contact with a tyre barrier around the back of the circuit.
Both Von Ryan entries made Superpole, with Alvaro Parente slotting the second 650S into 12th.
The McLarens join five BMWs, four Audis, three Mercedes, three Bentleys, two Ferraris and an Aston Martin in Superpole.
Remarkably, the top 24 cars were all within a second of the fastest time on the near two and a half minute lap.
The top Kessel Ferrari ended up third fastest, driven by Andrea Piccini, who shared the 458 with Craig Lowndes last year.
Lowndes and fellow Australians David Russell, Steve Owen and Roger Lago have missed out on a start in this year's event following Lago's heavy Carrera Cup crash in Townsville.
CLICK HERE for the full combined qualifying result.