Paraguay's team doctor Miguel Romero found that Aguilar's blood had shown a decrease in its ability to clot properly, and has advised that the defender return to Mexico where he currently plays for Tijuana.
Manager Victor Genes has called up Matias Perez as a replacement for Friday's match in Asuncion, which will see the bottom two sides of the South American qualification section go head-to-head.
Malaga striker Roque Santa Cruz flew in to join his team-mates late on Tuesday and was due to take part in full training with the rest of the squad on Wednesday.
Paraguay - who reached the quarter-final of the 2010 World Cup, where they were eliminated by eventual winners Spain - currently sit bottom of their regional pool, having taken just eight points from their 12 games so far.
And they will be hoping for a more positive result than in the reverse fixture in La Paz in June 2012, when a Pablo Escobar brace helped Bolivia to a 3-1 win.
Bolivia coach Xabier Azkargorta has a full 26-man squad to choose from after a trio of players joined up with their national team on Tuesday.
Jose Luis Chavez, Marcelo Martins and Ronald Raldes all flew in from their respective club bases in Mexico, Brazil and Argentina.
Azkargorta's side sit just two points above Paraguay in the standings, and trail fifth-placed Uruguay - who are currently on course for a play-off against Jordan or Uzbekistan for a place at Brazil 2014 - by six points.
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