Senna's Williams came up behind Vergne's Toro Rosso into the chicane at the end of the first segment.
The Frenchman - about to start his final flying lap - did not get out of Senna's way, earning angry gesticulations from the Brazilian.
That left Senna 17th, and when Michael Schumacher then grabbed 16th in the final moments, Senna was eliminated. Vergne qualified 17th.
Although Williams immediately reported the incident to the stewards, Senna said that even if Vergne was penalised it would be scant consolation.
"What's going to happen is that he's going to get a penalty probably but it's not going to change anything for me tomorrow," he said.
"That's where we are - 16th, 17th, 18th or whatever."
He believes it will be very difficult to make up ground at Suzuka.
"There are few places that are harder to overtake at than here," Senna said. "But we've been there, done that, so we just need to keep our hopes up."
Meanwhile Charles Pic has been reprimanded, and his Marussia team fined €5,000, after his near miss with Lewis Hamilton in final free practice.
Hamilton was left angry after he encountered Pic's slow car on the entry to the chicane while he was on a fast lap on Saturday morning.
After taking evasive action to prevent an accident, Hamilton radioed the team to complain about his rival.
Pic was summoned to see the stewards, who decided that he be reprimanded for failing to take into account Hamilton's approaching car.
Marussia was fined for not having informed Pic about the proximity of Hamilton.
And Nico Hulkenberg will lose five places on the starting grid following a gearbox penalty.
Force India had to replace the gearbox of Hulkenberg's car after the final practice session, in which the German crashed out when he lost of the rear end at the second Degner curve.
Hulkenberg qualified in 10th position.