Victory for Ajax was not enough as Dnipro Dnipropetrovsk secured their passage to the Europa League quarter-finals on away goals.
Ajax were looking to overturn last week's 1-0 defeat at the hands of Dnipro, and Anwar El-Ghazi went close early on, forcing goalkeeper Denys Boyko into a fine save.
Against the run of play, Nikola Kalinic unleashed a strike from the edge of the box, but Jasper Cillessen tipped the effort away for a corner.
Dnipro, who had lost just one of their five Europa League away games this season, continued to frustrate Ajax as the hosts struggled to find a vital opening.
Ajax enjoyed a strong spell of pressure, with Arkadiusz Milik's header the closest the hosts came to opening the scoring in the first half.
On the hour mark, 18-year-old Riechedly Bazoer levelled the tie on aggregate, dispossessing left-back Egidio before driving down the field and slotting past Boyko.
Roman Bezus went close with a headed effort following Yevhen Konoplyanka's cross, but his attempt bounced narrowly over the bar.
Bazoer saw another attempt blocked by Boyko, and neither side could gain the advantage they needed within 90 minutes.
Heading into extra time, it was Konoplyanka who gave Dnipro the aggregate lead, cutting in from the left before curling his effort beyond the reach of Cillessen.
Bruno Gama almost put the tie beyond doubt but Cillessen got down to fingertip the ball out for a corner.
Mike van der Hoorn gave Ajax a slim chance, scoring with just three minutes left, but Dnipro held out at the Amsterdam ArenA to qualify for the next round.
