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The Albiceleste have already qualified for Qatar 2022 with five matches to play in the CONMEBOL section.
Scaloni explained at a news conference on Thursday (AEDT) he had "completed the isolation" but had not received the negative test he required to enter Chile.
With assistant Pablo Aimar also absent as a close contact, coaches Walter Samuel, Roberto Ayala and Diego Placente are set to lead Argentina on Friday.
"Both Aimar and I are not going to be able to be part of the delegation," Scaloni said. "Pablo has been in his house for several days due to [being a] close contact.
"I completed the isolation several days ago, but I continue to test positive. To enter Chile you need a negative [test result].
"Walter Samuel, Roberto Ayala and Diego Placente are going to be present as part of the coaching staff."
Scaloni also confirmed players Alexis Mac Allister and Emiliano Buendia will miss the game, with the former testing positive for COVID-19 and the latter a close contact.
After its trip to Chile, Argentina is due to play at home to Colombia on Wednesday.
