English Premier League club Manchester City, managed by former Barca boss Pep Guardiola, were reported to have tabled a bid earlier this year for the 30-year-old, who scored 37 goals in La Liga and 11 times in the Champions League last season.
Messi's father and agent Jorge opened negotiations with Barcelona officials last December, but their talks on the player's eighth professional contract there progressed slowly.
The player joined the Catalan giants at the age of 13, made his debut in 2004 and has been there ever since, winning 30 major honours including eight domestic league titles and four Champions League trophies.
The No.10 has notched a record 507 goals for Barca in all competitions and is La Liga's record all-time scorer with 349 goals.
Messi married childhood sweetheart Antonella Roccuzzo in their native Argentina last week and is set to put pen to paper on his new deal at Barcelona when he returns from his honeymoon later this month, the club said.
"FC Barcelona and Leo Messi have agreed on a contract renewal that will keep the Argentinian at the club until June 30th, 2021," a club statement read.
"The club is very happy with both the renewal and the commitment of Messi, the best player in history, who has played his full professional career at Barca and has led the team to an era of extraordinary success."
Local media reports suggest Messi will remain the club's highest earner, while his buyout clause has been increased to 300 million euros ($340.08 million).
NEW DEALS
The player follows in the footsteps of team mates Luis Suarez and Neymar, who signed new deals last season.
Messi was about to enter his last year with the club before the new contract was agreed.
Messi and his father remain embroiled in a tax fraud case in Spain after a Catalan court last July found them guilty on three counts of fraud from 2007 to 2009 to the tune of 4.1 million euros (3.56 million pounds) on image rights.
The two were handed 21-month prison sentences but may have that substituted for a fine after prosecutors said they were open to dropping the jail terms. Neither are expected to go to jail as under Spanish law sentences of less than two years can be served under probation.
The judge in charge of the case will make a decision bearing in mind the prosecutor's recommendations. Judges usually follow the state prosecutor's guidance in Spain.
The case was one of the first high-profile investigations by Spanish authorities into top football players' tax affairs.
The state prosecutor earlier this month accused Real Madrid striker Cristiano Ronaldo of knowingly using a complex business structure to hide image rights income in Spain. Ronaldo has denied any wrongdoing.
(Reporting by Joseph Cassinelli and Sudipto Ganguly; Editing by Hugh Lawson)
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