Lewis Hamilton's troubles continued on Saturday after missing out on pole position at Suzuka.
Even though Red Bull has utterly dominated qualifying in 2011, Jenson Button dominated the practice sessions at Suzuka and the sister McLaren was holding provisional pole until the closing seconds of Q3.
As Vettel and Button went quicker on their final attempts, however, Briton Hamilton failed to start his flying lap before the chequered flag flew.
He looked gutted in parc ferme and the television unilaterals, insisting he still had a couple of tenths of pace in store for his last attempt.
Hamilton said he was "attacked" at the end of the out-lap by Mark Webber and Michael Schumacher, describing their moves as "dangerous".
"We told him not to back up and let so many cars by. Unfortunately he got hussled at the last corner," McLaren team boss Martin Whitmarsh said on BBC 1.