Hamilton's Mercedes team-mate Valtteri Bottas, who was the previous record holder with his lap for pole position past year, was third-quickest ahead of Sauber-bound fellow-Finn Kimi Raikkonen in the second Ferrari.
Informed of his imminent stewards' investigation, Vettel defended his actions.
Vettel said his weighbridge incident had happened because he was eager to get back to the pits. Bottas starts on the super-soft tyre, which should offer better grip away from the line than the softs fitted to Vettel's Ferrari.
Vettel trailed the Briton by just 0.093s, although his P2 was later under threat as he was summoned by the stewards for allegedly "destroying the scales" at the FIA weighbridge, after failing to turn off his engine as required. "They shouldn't call us like that. I wanted them to hurry up", said Vettel.
"I don't know if I would be doing Valtteri any favours in giving him a win", he added. It's clear what happened. "I think it's unfair if somebody is pulled in".
But Britain's most decorated Formula One outfit - indeed the team to have won more races in Brazil than any other - are in freefall with Alonso's team-mate, Stoffel Vandoorne, last of the 20 runners.
During Q2 he blocked both Kimi Raikkonen and Sergey Sirotkin on track, although neither incident was being investigated at the time of writing.
The drivers were all preparing for their first flying laps and Hamilton suddenly saw the Russian coming up behind him at much higher speed approaching Turn 12. Renault have found Interlagos' challenging final sector a tough ask this weekend, and they were unable to climb out of Q2 as Hulkenberg could only go 14th fastest, with Williams' Sirotkin finishing up bottom of the pile - although he will move up at least one spot due to Ocon's gearbox penalty.
"The stewards reviewed the video evidence from the on-board camera and pit lane CCTV, viewed team engine telemetry and heard from the driver of auto 5 (Sebastian Vettel) and team representative", a statement said.
"Yes, I definitely don't want to win if it's given to me", he said. Valtteri was ahead of me and he was backing off to get his gap so I had to back off. So it's up to us to find a fix for it and make sure it doesn't happen again, but it's not so simple to find and fix it as it sounds. "My last lap wasn't that good, to be honest".
"It is about how we're managing the tyres, we know we've made mistakes and we hope not to repeat them".
For his part, Bottas doesn't want to win a race through team orders.
Ericsson has been dropped by Sauber for next season and is to race in Indycars in the U.S., although he will remain the team's reserve driver.
Pierre Gasly, who will succeed Ricciardo at Red Bull, was ninth for Toro Rosso and Charles Leclerc, the Monegasque prodigy who will join Ferrari next year, was 10th for Sauber.
Fernando Alonso's F1 career continues to fade out with a fizzle, McLaren having the slowest vehicle in Brazil and the Spaniard able to put it only 18th.