Ricciardo qualified 16th to be the first car to miss the cut at the end of the opening segment of the three-part qualifying session.
His Qualifying 1 best of 1:43.547s proved just 0.075s slower than Fernando Alonso, who was 15th at the end of the segment but went on to qualify eighth.
Yuki Tsunoda in the other RB was two-tenths faster to escape the first cut and will line up 12th for Sunday’s race.
Following the session, Ricciardo was frustrated not to have progressed, pointing to a mistake a Turn 4 on his final lap.
“It wasn’t a terrible lap, it really wasn’t,” he said.
“I went in a bit deep in Turn 4, so kind of locked the rear a bit and that cost me some exit.
Secure your spot today.
“That corner was one where I probably left maybe a tenth on the table.
“But then I heard there was a little but in the castle section.
“Honestly, the lap was not perfect, but I’d say good. But I think everyone put in a pretty good lap and it just wasn’t good enough.”
Track evolution was especially strong during qualifying, with Ricciardo pulling himself out of the danger zone with his final flying lap.
However, as others improved, he was quickly bundled back into the bottom five.
“Would have love to not made that little error and been in here and tried to find a bit more out of it,” he said.
“Looking at the times, actually I think Q3 was not fully out of reach.
“But anyway, I don’t want to say that when I’m out in Q1, so try and do something tomorrow.
“Just missed a little bit today.”
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Ricciardo ended Friday’s running looking to roll back some of the set-up changes made between Free Practice 1 and Free Practice 2.
That left him 14th in the final hour of practice, though two red flags hampered running in that session.
The Australian also has a new floor on his car this weekend as RB delivered another instance of the upgrade Tsunoda debuted in Italy last time out.
While the Japanese driver was displeased with the floor there, work carried out on Friday in Azerbaijan has seen both RB drivers elect to keep the new part on their cars.
“There was a bit of cross-car stuff and then we both went with the same now,” Ricciardo explained of the floor analysis and decision.
“I think everyone’s happy with it. Yuki started with the other one, now he’s gone to it and he seems pretty happy.”
While Ricciardo qualified 16th, he’ll likely start 15th courtesy of Pierre Gasly.
The Alpine was referred to stewards for a fuel flow breach, which is expected to result in disqualification from the session.
Gasly had qualified 13th, meaning Ricciardo stands to inherit a place on the grid for the race.
The Azerbaijan Grand Prix begins at 21:00 AEST.
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