The Finn, who has yet to win this year, gave up nearly certain victory to Hamilton at the Russian Grand Prix under team orders but Hamilton was insistent that Mercedes would not use them in Bottas's favour in Brazil.
Vettel, though, faces an investigation after failing to follow stewards' instructions at the weighbridge.
To achieve that they'll need Bottas to perform and although he was unable to repeat his Q2 exploits by going top, to get his auto ahead of the sister Prancing Horse of Raikkonen will no doubt please his boss Toto Wolff.
Replays showed Vettel waving frantically at the FIA technicians as he arrived at the scales and urging them to complete the weighing process as quickly as possible. When the conditions are like that, it's not fair. "I wanted them to hurry up", said Vettel.
"All I can do is speak is for myself". It's clear what happened. "I think 18 was probably the best back in the day", he added.
It was the 10th time this year that Vettel had been quickest in FP3, but he has claimed only one pole position in his last 12 qualifying sessions.
Raikkonen also had to swerve to avoid him in another incident.
However, the proposal doesn't sit well with the British Mercedes driver.
"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 vehicle 5 (Sebastian Vettel) and team representative", a statement said.
Hamilton said: "Everyone was on an out-lap - me, Sergey and everyone in front of me". Valtteri was ahead of me and he was backing off to get his gap so I had to back off.
Carlos Sainz dropped out of qualifying in Q1 after the Renault driver was caught out by a late flurry of lap times that saw him slip down the order.
"But he wasn't on a lap, so I don't know what his thinking was".
"Obviously, along the way, something went wrong and we need to learn from it".
"That's what we're trying to do... and we'll see in two races' time". Vettel's team-mate Kimi Raikkonen qualified fourth.
Haas were best of the rest in the morning, with Romain Grosjean and Kevin Magnussen seventh and eighth.
Fernando Alonso's F1 career continues to fade out with a fizzle, McLaren having the slowest auto in Brazil and the Spaniard able to put it only 18th. Toro Rosso's Brendon Hartley, who had high hopes this weekend with Honda's Spec 3 engine, also narrowly missed out (by 0.011s to be precise), while McLaren pair Fernando Alonso and Stoffel Vandoorne joined Williams' Lance Stroll in suffering the familiar fate of opening-segment elimination.
Sky Sports F1 is the only place to watch every Formula 1 Grand Prix, qualifying and practice session live in 2018. "The weather was going up and down.Ferrari are very quick this weekend, but we did a lot of work to make sure we are ready". The last lap wasn't that great so I didn't know that I had pole and I was so grateful when I heard I did.
Vettel set his Q2 time on soft tyres, with Hamilton using supersofts, giving the Ferrari man an advantage on the opening stints in Sunday's race. "I tried. The first sector was so good".
Hamilton and Vettel provided the main talking points of the session, with the former fortunate to escape the immediate attention of the stewards after almost colliding with the Williams of Russian Sergey Sirotkin in the second phase.