Geraint Williams' side could no longer advance from Group Three after their home defeat to Armenia last month, but had been looking to end the campaign with a good performance against the table toppers in Jablonec nad Nisou.
But, after a bright start, those hopes were firmly dashed as Filip Novak, Tomas Wagner, Ondrej Vanek and Stanislav Tecl (2) helped the hosts to an emphatic win.
Billy Bodin had fired wide of the target when well placed during the early stages for the visitors, with Jake Cassidy another to waste a decent chance.
And once the Czechs got into their stride those misses proved costly.
They took the lead in the 17th minute as Novak found the net after the visitors failed to clear a corner.
Wales held their own until the hour mark but matters went rapidly downhill once Wagner doubled the home side's lead.
Vanek then tapped in the third after goalkeeper Dai Cornell had done well to keep out Pavel Cmov's shot.
Tecl then rounded off the scoring as he netted from the spot after Adam Henley had fouled him, before bagging the fifth with 11 minutes remaining.
Wales were even denied a late consolation as Jake Taylor saw his effort saved.