The Uruguayan FA was additionally fined 50,000 Swiss francs for the behaviour of its supporters and team members.
Uruguay's Fernando Muslera and Jose Maria Gimenez were hit with four-match bans by FIFA on Friday, while Diego Godin and Edinson Cavani were suspended for a game each after they confronted the referee following their World Cup match against Ghana.
FIFA launched proceedings against the players who angrily harangued the referee after crashing out of the tournament in Qatar, despite beating Ghana 2-0 in their final group match on December 2.
In the Group H deciders, Uruguay had one foot in the last-16 before South Korea scored in stoppage time to beat Portugal 2-1 and went through by virtue of scoring one goal more than the South Americans over their three matches.
German referee Daniel Siebert decided not to award penalties for tackles on Darwin Nunez in the opening half and Cavani in the dying minutes, with striker Luis Suarez saying after the game that FIFA was "against Uruguay".
The players will also have to carry out football-related community service, and will pay fines of up to 20,000 Swiss francs ($21,701).
The Uruguayan FA was additionally fined 50,000 Swiss francs for the behaviour of its supporters and team members, FIFA said.
Uruguay were also ordered to partially close their stadium for their next FIFA "A" international match as hosts.
