Messi was handed a three-month ban from international football in August for accusing South America's governing body CONMEBOL of "corruption" during the Copa America.
After being controversially sent off in Argentina's third-place play-off win over Chile in July, Messi did not appear to collect his medal and the five-time Ballon d'Or winner later explained that he did not want to "be part of this corruption, this lack of respect towards the whole Copa".
Messi also blasted the officiating at the competition after Argentina's semi-final loss to host Brazil, before then suggesting referees and the VAR (video assistant referee) would favour Tite's men against Peru in the final, which the Selecao won 3-1.
The Argentina skipper has missed friendlies against Chile, Mexico and Germany, and he will sit out Monday's (AEDT) clash with Ecuador ahead of next month's return.
Asked about Messi, Scaloni said: "Messi is not here due to suspension.
"Sergio Aguero is not here because he's been carrying a problem and has not been training 100 per cent with his club.
"Surely both will be here next month."
Argentina is coming off a 2-2 draw away to Germany on Thursday (AEDT), a game in which Scaloni's men overturned a two-goal deficit in the second half.
Scaloni has already named his line-up for the match against Ecuador, with Agustin Marchesin, Juan Foyth, German Pezzella, Walter Kannemann, Marcos Acuna, Nicolas Gonzalez, Rodrigo De Paul, Leandro Paredes, Lucas Ocampos, Lucas Alario and Lautaro Martinez starting.
"The idea is to play with attacking players. With players that get to the penalty area," Scaloni said.
"We believe that this is the right way. We take decisions thinking about what is best for the team."