Liverpool were still without leading goalscorer Milan Baros, who was ruled out with a hamstring injury.
Fabio Cannavaro struck the post late on, while Milan Baros was off target with Liverpool's best chance.
Milan Baros claimed a penalty after he was upended by Steve Foster, but the Czech Republic's plea was ignored.
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Both sides made half time changes, with Milan Baros replacing Heskey and Pompey replacing Dejan Stefanovic with Richard Hughes.
The Czechs had the best two chances in the first half but Radoslav Kovac and Milan Baros sent their headers wide.
Owen's place was taken by Milan Baros, who scored Liverpool's second goal as well as causing Paolo Maldini problems all night.
Milan Baros' second-half penalty gave Galatasaray a 1-0 victory over Hertha Berlin as the Turkish side ensured their qualification from Group B.
Speculation about Owen returning to Anfield has been fuelled by reports that Liverpool forwards Milan Baros and Djibril Cisse may leave the club.
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Second-half substitute Milan Baros then shot wide before strike partner Koller put the win beyond doubt when heading home Jaroslav Plasil's 74th-minute corner.
As so often this season, Liverpool packed their midfield, leaving Milan Baros up on his own in attack in an attempt to stifle Arsenal.
Redknapp, who managed Defoe at West Ham, had already bolstered his forward line with the loan signing of Lyon striker Milan Baros during the January transfer window.
Chasing a two-goal deficit, the visitors withdrew John Utaka for on-loan striker Milan Baros, who was denied his first Portsmouth goal when Hart made a fine stop.
Former Liverpool star Harry Kewell, a team-mate of Neill's in the Australia team, and ex-Aston Villa striker Milan Baros are already playing at the Ali Sami Yen Stadium.
But it took them only seven minutes of the second half to get back on level terms, Angel scoring from substitute Gabriel Agbonlahor's cross after a positive run from Milan Baros.
Cech then denied Simao Sabrosa, and at the other end Tomas Ujfalusi's header flashed past the past from another corner with Sionko and Milan Baros both just failing to make a vital connection.
Pompey fired out of the blocks in the second half, Defoe volleying a Milan Baros cross straight at keeper Craig Gordon and then forcing the Scot into action again with a 20-yard drive.
In Group F, Galatasaray strolled to a 3-1 victory away to Panathinaikos in Athens as Brazilian summer signing Elano scored twice -- one a deflected free-kick -- and set up another goal for Czech striker Milan Baros.
Paolo Guerrero was sold to Hamburg and Beckenbauer claims further departures to the north may be on the cards as their Bundesliga rivals are in the market for a striker, having failed to land Milan Baros or Patrick Kluivert.
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