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The Barcelona captain argued that he should be allowed to leave the club through the free clause in his contract, but the Spanish club insisted that the clause had expired.
Messi, who was heavily linked with Manchester City, remained at Barcelona after refusing to take the club to court over his disputed contract clause.
Puyol, 42, was one of those who was shocked by the news and even sent his best wishes to Messi during his transfer saga with Barcelona in the summer.
"Respect and admiration, Leo. All my support, friend," he tweeted in August.
The Barcelona legend has now branded Messi not only as a "huge asset for La Liga," but also "one of the best in the world."
Puyol told reporters: "Like any fan, I did not want Messi to leave, but this is football.
"In the end, he decided to stay. He recently said that he is motivated, that he wants to win and we hope he can continue with us for many years.
"He is a huge asset for La Liga, he is one of the best in the world."
City chief Omar Berrada has suggested that the Premier League club could make a move for Messi next summer should he not sign a new deal with Barcelona.
"He's an amazing talent, he's somebody that can make a significant impact at any club in the world on and off the pitch immediately," he told the Manchester Evening News.
"He's the best player in the world, he's the best player of his generation. I think any club in the world would like to explore the possibility of him joining their team.
"The fact that it was commented that he wanted to come to play for City just shows you how far the team has come over the last [few] years where the best talent of his generation and potentially saying he wants to come and play for us.
"It's hard to guess what could happen. If you think back to those two weeks where everything played out at Barcelona, it's almost impossible to guess what will happen next summer."
Featured Image Credit: PA
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