Suárez bid farewell to Barcelona's fans in an emotional news conference on Thursday. He leaves Camp Nou as the club's third leading scorer with 198 goals. The Uruguayan helped Barcelona win 13 titles since arriving in 2014 from Liverpool, including four Spanish league trophies and the Champions League in 2015.
Suárez forged a dynamic scoring duo with Messi over the years, and the two South Americans became neighbours and fast friends, along with their families.
"I was accepting the idea (of your departure), but not until I entered the changing room did I realise what it means," Messi wrote. "How difficult it is going to be not sharing each day with you, both on and off the field. We will miss you very much. These have been many years of many mates, lunches, dinners ... many things I won't forget from all those days together."
Barcelona transferred Suárez to Spanish league rival Atlético for up to 6 million euros ($NZ10.7m) in variables. He signed a two-year deal with the club after passing a medical exam on Friday.
Messi tried to leave the club he has been a part of for 20 years after the debacle against Bayern, but Barcelona replied he must finish the final year of his contract.
Suárez also took Messi's side in the dispute on Thursday when he said, "I have to accept it if the club decides it is time that I go, just like the club should accept it if a player wants to leave."
He thanked Messi for his parting message in a reply on Instagram, saying "I love you very much my friend" and urged Messi not to let "2, 3 or 4 tarnish how gigantic you have been for the club and the world of football."
Messi has given up trying to leave this season. He has vowed to play his hardest for the team while he remains — even if he is even more disgruntled after Suárez's departure.
Messi's comments are the latest run-in between him and the club board.
Club president Josep Bartomeu has called for elections in March, when he cannot run again, but he is also facing a censure referendum that could oust him and his board in the coming weeks. The clashes with Messi will likely weaken his chances of finishing the season.