The players had been given time off from midday to 10pm on Tuesday, after morning training, Borghi said.
"Five players arrived 45 minutes late and not in a state adequate to a professional player. So I took the decision to withdraw them [from the squad]," the Argentine coach told a news conference.
He named the five as midfielders Arturo Vidal of Juventus, Jorge Valdivia of Palmeiras and Carlos Carmona of Atalanta, Birmingham City winger Jean Beausejour and West Bromwich Albion defender Gonzalo Jara who is on loan at Brighton & Hove Albion.
"These are the players who did not comply, not with a written agreement but a verbal agreement," the Argentine coach added.
Defender Jara had already been ruled out of the matches due to a knee injury.
Local media had broken the news in the morning with some speculating that Borghi, who then called the news conference, might announce his resignation.
Borghi's squad are preparing for South American ties against Uruguay on Friday and Paraguay next Tuesday.
Chile, who lost their opening qualifier 4-1 to Argentina in Buenos Aires last month before bouncing back to beat Peru 4-2 at home, travel to Montevideo on Thursday to face South American champions Uruguay. They host Paraguay in Santiago.
All five players played in both October ties.
As replacements, Borghi called up Chile-based players: Universidad Catolica midfielders Felipe Gutierrez, Francisco Silva, Fernando Meneses and Milovan Mirosevic and defender Jose Rojas of Universidad de Chile.
