Leading 1-0 from the first leg, Arsenal trailed 1-0 at half-time and survived an Antonio di Natale penalty miss with the score at 1-1 before Theo Walcott scored to lift the pressure.
Twice former European champions Benfica joined them with a 3-1 win over Twente Enschede and Olympique Lyon made it 12 appearances in a row by holding out for a 1-1 draw at Rubin Kazan in the play-off second legs.
The five completed the line-up for Thursday's group stage draw in Monaco.
Trabzonspor were named by UEFA as Turkey's representatives earlier on Wednesday after Fenerbahce were pulled out by the Turkish FA over the country's match-fixing scandal.
Arsenal's 3-1 aggregate win was a relief for manager Arsene Wenger after a difficult start to the season, with injuries adding to the departures of Cesc Fabregas and Samir Nasri.
"It's relief and pride as well," he told Britain's ITV . "We had our backs to the wall but there was only one team on the pitch in the second half.
"We showed great belief in the way we want to play football. It was very important tonight, not for financial reasons as many people have been saying, but more because we want to play at the top level."
Arsenal were over-run for much of the first leg and fell behind when Di Natale, who had already hit the post, met Giampiero Pinzi's cross with a looping header in the 39th minute.
Lyon's progress was far less comfortable at Rubin Kazan where Bebras Natcho volleyed in Obafemi Martins' pass with 13 minutes left, leaving the Russians one goal from an away goals win.
Marek Bakos knocked home Petr Jiracek's cross from close-range to level in the 67th minute, his sixth goal of the qualifiers, and Michal Duris struck deep into stoppage-time to complete a 5-2 aggregate win.
