Gerardo Pelusso also opted against recalling striker Roque Santa Cruz, in good form for Champions League quarter-finalists Malaga, to face the coach's home country Uruguay in Montevideo on March 22 and Ecuador in Quito six days later.
Santa Cruz and Villar were a key part of the Paraguay side that reached the quarter-finals for the first time in South Africa in 2010.
Villar was an unused substitute in October when Paraguay, bottom of the South American group, ended a run of four defeats with a 1-0 home win over Peru, his place having been taken by Diego Barreto.
Santa Cruz, who last played for his country in the 3-1 defeat in Argentina in September, was dropped for two qualifiers in October.
Paraguay, who hired Pelusso last year after sacking Francisco Arce, are in serious danger of failing to qualify for the finals for the first time since 1994.
The top four teams progress to the 2014 finals in Brazil and the fifth-placed side face Asia's fifth-ranked nation in a two-legged play-off.