Ajax beat FC Groningen 2-0 in Thursday's semifinal and were paired up with FC Utrecht, who beat sc Heerenveen 3-2 at home that same evening.
Interim manager Óscar García shuffled some more pieces in what's likely his last game at the helm, with Kasper Dolberg and Youri Regeer returning to the starting XI in place of Wout Weghorst and Sean Steur.
The first big chance was for the visitors, who beat Ajax in Amsterdam just two weeks ago thanks to Mike van der Hoorn's injury-time header. Van der Hoorn stepped up early in the game for Utrecht this time, but missed Maarten Paes' goal by a hair inside two minutes.
It proved the biggest chance of the half, with Souffian El Karouani, Steven Berghuis, Aaron Bouwman, and Lucas Rosa firing at goal, but all failing to break the deadlock before the break.
Ajax gained momentum late in the first half and carried it into the second half, with Aaron Bouwman coming close during a corner and Jorthy Mokio hitting the crossbar early.
With Utrecht only coming close through Sebastien Haller, who missed a big chance after Van der Hoorn extended a free kick with his head, Ajax failed to put Utrecht under much pressure themselves, with 90 minutes not enough to determine who plays in the Conference League.
Ajax finally struck first in the 96th minute through Davy Klaassen, who opened the scoring again, this time by taking a loose ball from a corner on the bounce and burying it into Vasilis Barkas' bottom corner.
Mika Godts nearly put the game to bed before half-time of added time, but hit the crossbar after Barkas got his fingertips on the Belgian's fiery attempt.
As often was the case with Ajax this season, the Amsterdam side came out of the break lacking in intensity and squandered the lead within a minute through Gjivai Zechiël, who, like Klaassen, picked the ball out of the air and left Paes without a chance.
The woodwork proved not to be on Ajax's side once again following Zechiël's goal, with Maher Carrizo's header hitting the post.
Heated penalties
As players dropped like flies in the Volendam heat and following a 10-month season, time ran out for both sides to make a difference on the pitch and the Dutch play-offs were to be decided on penalties.
Utrecht and former Ajax striker Sebastien Haller stepped up first, but missed as Paes reacted aptly and caught it in his bottom corner. With the advantage on their side, Ajax took the lead through captain Davy Klaassen to deal the first real blow. The teams exchanged scored penalties for the next six tries, as it came down to the last seconds of the best-of-five.
With his final kick for the club, FC Utrecht's Souffian El Karouani was stopped by Indonesia's Maarten Paes, who officially saved Ajax's season.
With the relieving win in Volendam, Ajax have officially secured a spot in the UEFA Conference League qualifiers, avoiding a disaster by keeping the 1989/90 season as the last time the Amsterdam giants failed to qualify for European football altogether. Ajax will now join the UEFA Conference League in the second qualifying round in July.