Aguero announced his retirement from football with immediate effect due to heart issues, which started with an incident in a LaLiga clash last month.
Tributes have been coming in from all over, but Messi took to social media to send Aguero a lengthy emotional message after a glittering career.
"Practically a whole career together, Kun.... We've had some great moments and others that weren't so great, but all of them have made us grow closer and become better friends. And we're going to continue spending them together off the pitch," Messi wrote in an Instagram post.
"With the great joy of lifting the Copa America just a little while ago, with all the achievements you obtained in England.... And the truth is that now it hurts a lot to see how you have to stop doing what you love the most because of what happened to you. I'm sure you will continue to be happy because you are a person who radiates happiness and those of us who love you will be there for you. Now a new stage of your life is beginning and I am convinced that you will enjoy it with a smile on your face and with all the enthusiasm that you put into everything.
"All the best in this new stage! I love you very much my friend, I'm going to miss a lot being with you on the pitch and when we meet up with the national team."