Neymar's proposed €222 million switch to the French capital swiftly gathered pace on Wednesday as he was granted permission to miss training and tie up his future.
The Brazil star informed the Barcelona board and his team-mates of his intention to leave and Messi, who lined up in the all-conquering "MSN" forward line alongside Neymar and Luis Suarez, paid tribute to his colleague in an Instagram post.
"It was a great pleasure to have shared all these years with you, friend," Messi posted alongside a photo montage of the pair.
"I wish you a lot of luck in this new stage of your life. See you, I love you a lot."
Messi signed a new contract at Barcelona last month, reportedly worth €565,000 per week, tying him to Camp Nou until 2021.
The five-time Ballon d'Or winner's continued presence at Barca is rumoured to have been a factor in Neymar's decision to leave, with his inner circle reportedly of the opinion that he will not be considered the best player in the world until he has the opportunity to step out of Messi's shadow.
Neymar scored 105 goals in 186 games for Barcelona, with 20 of those strikes coming from Messi assists. He set up Messi on 22 occasions out of a total 59 assists.