Brazil captain Neymar was handed a four-match suspension by Conmebol following his red card and subsequent verbal attack on a referee after his side's 1-0 defeat to Colombia this week.
Argentina skipper Messi refused to be drawn on the controversy surrounding the decision to ban his Barcelona team-mate from the remainder from the tournament but admitted it is a blow for the 23-year-old.
"I do not want to comment on Neymar. He's a friend," Messi, who starred alongside the Brazilian as Barca romped to a treble this season, said after Argentina's 1-0 win over Jamaica.
"I regret the punishment he was given and that he cannot participate any further in the Copa America.
"He is a very important player for Brazil. I know what it means to them to have him on the field."
Brazil have the right to appeal the suspension but even a successful plea would likely only see his suspension dropped to three games, which would still rule him out until the final.
Brazil face Venezuela on Sunday in their final group game hoping to secure a place in the quarter-finals, with all four teams from Group C locked on three points.