AC Milan center-back Zapata has not played since suffering a hamstring tear in late April while Deportivo Cali midfielder Aguilar is also recovering form a leg muscle problem, reports Xinhua news agency.
In a statement on Monday, the Colombian football federation said both players had stepped up their recovery after missing the team's 0-0 draw with Egypt in Italy on Friday.
As expected, Colombia will be led by Monaco striker Radamel Falcao and Bayern Munich midfielder James Rodriguez.
Falcao, 32, will be making his first World Cup appearance, having suffered a serious knee injury before the 2014 tournament in Brazil.
There was no place in Pekerman's squad for Boca Juniors playmaker Edwin Cardona while Santa Fe youngster William Tesillo and veteran forward Teofilo Gutierrez also missed out.
Colombia will begin their campaign in Russia against Japan on June 19 before facing Poland and Senegal in Group H.
The squad:
Goalkeepers: Jose Cuadrado (Once Caldas), David Ospina (Arsenal), Camilo Vargas (Deportivo Cali)
Defenders: Santiago Arias (PSV), Frank Fabra (Boca Juniors), Yerry Mina (Barcelona), Johan Mojica (Girona), Oscar Murillo (Pachuca), Davinson Sanchez (Tottenham), Cristian Zapata (AC Milan).
Midfielders: Abel Aguilar (Deportivo Cali), Wilmar Barrios (Boca Juniors), Juan Cuadrado (Juventus), Jefferson Lerma (Levante), Juan Quintero (River Plate), James Rodriguez (Bayern Munich), Carlos Sanchez (Espanyol), Mateus Uribe (Club America).
Forwards: Miguel Borja (Palmeiras), Radamel Falcao (Monaco), Jose Izquierdo (Brighton and Hove Albion), Luis Muriel (Sevilla).
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
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