Victory leapfrogged the Czechs over Scotland who went down 3-1 to runaway group winners Spain. Spain ended with 24 points with the Czech Republic a distant second with 13.
Michal Kadlec opened the scoring from the penalty spot in the second minute after Andrius Skerla pulled back Daniel Kolar. Jan Rezek doubled the lead in the 16th minute from a close range and struck again on the stroke of half-time with a header.
Darvydas Sernas pulled one for the hosts from the spot in the 68th minute after being fouled by Roman Hubnik who was shown a red card but Kadlec converted his second penalty of the evening five minutes from the end of normal time.
The Czechs will find out who they will face in the play-offs when the draw is made on Thursday.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.