Viktoria Plzen booked their place in the Europa League knockout stage, despite conceding a late equaliser at Academica on Thursday night.
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Pavel Horvath's penalty in the 55th minute looked set to earn the Czechs a deserved win, only for Edinho to net a spot-kick of his own two minutes from time.
The draw was still enough to send Plzen through and Academica out, though, as it moved the visitors five points clear of their third-placed opponents in Group B.
The hosts started brightly and Alexandre Silva Cleyton's right-footed shot from 12 yards was superbly saved with his feet by goalkeeper Matus Kozacik.
Both sides appeared content to try their luck from range, with Academica's John Ogu and Plzen's Horvath having shots from well outside the area saved.
There was little entertainment on offer in an uninspiring first half, but it threatened to come to life in the closing moments.
Ogu's drilled effort from the left side was parried impressively by Kozacik, while at the other end Ricardo Nunes pushed away a Vladimar Darida effort from inside the area.
The opening goal, when it arrived, came from the penalty spot.
Manuel Joao Dias fouled David Stipek and Horvath stepped up to slot the spot-kick low into the right corner.
The Czech side almost made it two in the 65th minute when Vladimar Darida met Radim Reznik only to see his shot denied by the feet of Nunes.
The visitors continued to create chances and again Nunes had to be alert, this time to parry a brilliant curling free-kick from Vaclav Prochazka.
The Portuguese were handed a way back into the match at the death when Marian Cisovsky fouled Salim Cisse in the area and Edinho levelled coolly from the spot, but it was not enough to prevent them going out.