Messi missed two matches due to a knee injury before returning for Paris Saint-Germain in their Champions League win over Manchester City and last week's shock Ligue 1 loss at Rennes.
The six-time Ballon d'Or winner is away on international duty with Argentina, who will visit Paraguay on Thursday, and Messi has been given the all-clear to play.
"Messi trained with us yesterday [Tuesday] without any problems and this morning too, so he's fine to play," Scaloni told reporters on Wednesday.
"Which is the most important thing and he's like the rest of the group, wanting to get together and do the best for the national team. Regarding his injury, it is evident that he has played two games before coming here and this is fine."
During the last international break, Messi surpassed Brazil great Pele as the all-time leading goalscorer for a South American nation.
Messi scored a hat-trick for Copa America champions Argentina in their 3-0 qualifying win over Bolivia last month, the 34-year-old taking his tally to 79 international goals.
Argentina – second behind Brazil in the standings – remain unbeaten on the road to Qatar 2022 with five wins from their eight fixtures, while they extended their undefeated streak to 22 matches across all competitions.
"The challenge that we have, or that I have in this case as a coach, is that the team competes in all the games and, that the things that I know that are done well, do it again or strengthen them and that they can be improved and tried in training even if they are few, and try to put a lot of emphasis on that," Scaloni said.
"We believe that in a collective level the national team has a fairly regular performance and I think that at an individual level it is evident that we have players who decide matches, but in a collective level I think that we have improved a lot in that and that one of the things in which the team does is give the feeling that that is always why, because we work as a team and because whoever enters or leaves knows very well what they have to do and I think that is the most important thing.
"Then there are things to improve on like all teams and even more so that we have very few days together. But our feeling is that as a team we are doing well."