An own-goal from Seweryn Gancarczyk just three minutes into the final qualifying match was enough to see them beat Slovenia to top spot by two points.
Slovenia now have to settle for a two-legged play-off tie to reach the finals in South Africa, despite a 3-0 win away to San Marino.
Milivoje Novakovic gave the visitors a 24th-minute lead and goals from Dalibor Stevanovic and Marko Suler in the second period wrapped up a comfortable if not especially emphatic victory.
The results all meant that the match between the Czech Republic and Northern Ireland was to have no bearing on next year's finals line-up.
But Northern Ireland manager Nigel Worthington will take comfort from a creditable goalless draw at the Synot Tip Stadium.