Midfielder Valdivia, who has a long record of disciplinary issues, was given a four-match ban for vigorous protestations after the final whistle in Chile's 3-0 qualifying defeat by Uruguay.
Striker Vargas was banned for two matches for making obscene gestures to fans during the same game.
Chile's next four matches are against Argentina, Venezuela, Paraguay and Bolivia.
They lie fifth in South America's 10-team standings with the top four automatically qualifying for Russia 2018 and the fifth-placed side going into a playoff against a team from Oceania.
(Writing by Andrew Downie, editing by Ed Osmond)
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