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The 34-year-old Argentine forward's contract with the Spanish club expired in June, with Barcelona in talks to commit his long-term future to the Camp Nou.
Messi was prepared to take a staggering 50 per cent pay cut on his new contract amid Barcelona's financial problems.
However, Barcelona made a bombshell announcement on Thursday that the Argentina captain would not re-sign with the club due to "Spanish La Liga regulations on player registration."
The La Liga club's statement reads: "Despite FC Barcelona and Lionel Messi having reached an agreement and the clear intention of both parties to sign a new contract today, this cannot happen because of Spanish La Liga regulations on player registration.
"As a result of this situation, Messi shall not be staying on at FC Barcelona. Both parties deeply regret that the wishes of the player and the club will ultimately not be fulfilled.
"FC Barcelona wholeheartedly expresses its gratitude to the player for his contribution to the aggrandisement of the club and wishes him all the very best for the future in his personal and professional life."
According to Spanish newspaper Sport, Messi has been left 'emotionally destroyed' by Barcelona's inability to sign him to a deal.
The publication added that the Barcelona legend did 'not expect it at all.'
Transfer news expert Fabrizio Romano confirmed that Messi's father, Jorge, was recently in Barcelona to sign the contract, which would have kept his son at the Camp Nou until 2026.
He said that Barcelona had already prepared an official statement and announcement on Thursday evening to mark Messi's contract signing.
According to Romano, a 'total verbal agreement' had been reached between Barcelona and Messi for 'weeks.'
The 28-year-old Italian reporter revealed that Barcelona also face an issue in registering other players due to La Liga's financial rules.
Messi reportedly 'appreciated' Barcelona president Joan Laporta's transparency over the situation in a meeting.
But the crestfallen six-time Ballon d'Or winner was stunned by Barcelona's 'forced' decision after La Liga's position on the matter, according to Romano.
Paris Saint-Germain have reportedly wasted no time in opening talks with Messi, who previously turned them down this summer amid his desire to stay at Barcelona.