The Czechs headed into their final qualifier knowing they had to achieve a better result than the Scots managed against Group I winners Spain and, while Craig Levein's side never looked likely to cause an upset against the world and European champions, the result in Kaunas never looked in doubt either.
Michal Kadlec put the visitors ahead from the penalty spot within two minutes and Jan Rezek's double had them three up at the break.
The Czechs were reduced to ten men midway through the second half when Roman Hubnik saw red. Darvydas Sernas converted the resulting penalty, but another Kadlec spot-kick five minutes from time sealed a convincing away win.
The game could hardly have got off to a worse start for fourth-placed Lithuania, who conceded a penalty with less than a minute on the clock. Andrius Skerla earned a yellow card for a foul on Milan Baros and Kadlec unleashed a cool left-footed penalty into the top-left corner.
Chelsea goalkeeper Petr Cech had to be on his toes to preserve his side's lead in the fourth minute, tipping Sernas' shot around the post, but the action soon returned to the other end.
Baros almost doubled his side's lead just before the quarter-hour mark when his right-footed blast from the edge of the area struck the post, but the visitors did not have to wait too much longer for their second goal.
Galatasaray striker Baros was the provider, setting up Anorthosis Famagusta frontman Rezek to lash into the top-left corner in the 16th minute. Rezek got his name on the scoresheet for the second time just before the interval when he slid in to head home Jaroslav Plasil's cross.
Hubnik was sent off in the 67th minute for bringing down Sernas in the area, forward picking himself up to fire the penalty past Cech and reduce the deficit to 3-1.
However, the Czechs soon restored their three-goal cushion when Kadlec sent the third spot-kick of the night into the bottom-right corner after Ramunas Radavicius had fouled Tomas Pekhart, and the visitors - knowing Spain had done them a favour in Alicante - were able to celebrate their play-off place.