Messi broke down after tearing his thigh in the first-half, an injury which will keep him out of action for at least a month.
Deco said: "We saw him crying and this affected all of us. There is nobody like him, but he is very young and I am sure he will recover."
On the victory, the Portugal midfielder added: "We achieved our objective. Not all games are great, but the important thing here was to progress."