The Argentine netted the opening goal of the first leg, his 57th this season, but it was Ibrahimovic who had the last word as he set up a late equalizer.
But Diego Forlan pulled one back after 71 minutes -- incredibly Inter's first in 541 minutes -- before the Uruguayan set up Diego Milito for the equalizer.
The Czechs battled bravely for an equalizer, but Sionko saw his 83rd-minute header tipped over by Ricardo from yet another set-piece when it seemed he should have scored.