Australia lock Matt Philip scored twice to keep Pau in the French Top 14 with Saturday's 41-25 win over Montpellier in the final round of the regular season.
Philip, who made the last of his nine Wallabies appearances in December, crossed for his second try in the final moment of the game which sent Bayonne into a relegation play-off with Basque rivals Biarritz next weekend.
"We've done it. We'll remember that. It's massive what we've done. We stayed the masters of what we had to do," Pau captain Lucas Rey said.
"We're not world champions, but it's great," he added.
Stade Francais' 12-9 victory at Bayonne claimed the Parisians a play-off spot where they will play fellow French capital outfit Racing 92, who hammered Brive 55-12.
The other play-off will see Clermont, who beat La Rochelle 25-20, play Bordeaux-Begles, who lost 21-10 to Toulouse.
La Rochelle and Toulouse reached the semi-finals thanks to their results and will face the two winners from the play-off matches in two weeks' time.
At Stade du Hameau, Pau led 22-10 at the break as Pacific Islanders Aminiasi Tuimaba and Tumua Manu crossed before Philip opened his account for the season.
Montpellier fought back into the fixture and trailed by just two points with a quarter of the game left.
They were denied a try by the video referee and four minutes later Tuimaba scored to set up a tense final quarter of an hour with Pau knowing a sixth try and bonus point would move them above Bayonne.
Pau piled on the pressure and Philip's crashed over after 82 minutes.
The tension remained as Bayonne's game was yet to finish and Pau's players and coaches watched the final two minutes on a pitchside television as the Basque side failed to claim a draw against Stade Francais.
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Elsewhere, uncapped South African hooker Joseph Dweba played 41 minutes for Bordeaux-Begles a matter of hours after being named in South Africa's squad for the upcoming series against the British and Irish Lions.
France captain Charles Ollivon was helped off the field in Toulon's loss at Castres after 15 minutes with a serious knee injury.
French Top 14 play-offs (times GMT)
Friday June 11
Racing 92 v Stade Francais (1845)
Saturday June 12
Bordeaux-Begles v Clermont (1845)
Saturday 12 June
Biarritz v Bayonne (1530)