Enrique Vera put the South Americans ahead after 27 minutes and Cristian Riveros grabbed a second four minutes from time in a game of few chances at Free State Stadium.
The win puts Paraguay on four points and leaves Slovakia with one. World champions Italy and outsiders New Zealand, who have one point each, meet in Nelspruit later on Sunday.
In Image: Paraguay players celebrate after fellow team member Cristian Riveros, not visible, scored a goal
Coverage: FIFA World Cup