FIFA's disciplinary committee said it took the action "as a result of the non-payment of an outstanding debt" by Zimbabwe to coach Jose Claudinei Georgini, who left the job in 2008.
The decision was announced just as the first match in qualifying was kicking off in Asia. East Timor beat Mongolia 4-1.
Zimbabwe's removal spoiled FIFA's recent claim of a first qualifying campaign where all its member federations would play.
Zimbabwe was initially ordered by FIFA to make the outstanding payments to the Brazilian coach in August 2012. Disciplinary proceedings were later opened against the Zimbabwe Football Association on the request of Claudinei, FIFA said.
In April 2013, ZIFA was given 60 days to pay half the amount it owed Claudinei, and 120 days to pay the full amount. Zimbabwe was given a final grace period to settle the debt before being banned, FIFA said on Thursday in a statement.
Because it failed to make any payments, the FIFA disciplinary committee "ordered the expulsion of ZIFA from the preliminary competition of the 2018 World Cup (in) Russia," FIFA said.
FIFA said Zimbabwe did not immediately appeal its expulsion, but ZIFA's chief executive told The Associated Press later Thursday that the association would challenge the decision.
"It's a massive blow on Zimbabwean football," chief executive Jonathan Mashingaidze said. "We have already started engaging FIFA, and we are going to appeal against the decision."
Mashingaidze said the ZIFA leadership "inherited the debt" from its former board.
Zimbabwe's soccer body has severe financial problems, reflecting the dire economic situation in the troubled country.
ZIFA has sold off some of its facilities — including an artificial soccer turf reportedly donated by FIFA — to pay some of its debts. A tractor and furniture at a ZIFA training centre were also up for auction.
ZIFA needed the money after being ordered by a court to pay another former employee around $80,000 for unfair dismissal. Assets were also removed from the association headquarters on the order of the court.
Zimbabwe has never qualified for the World Cup. African qualifiers for the 2018 tournament are scheduled to start in October.
Last month, Russia coach Fabio Capello was finally paid his outstanding salary since June, thanks to a $6 million loan to the Russian Football Union by billionaire Alisher Usmanov.