It also reached agreements with two of its other top players, veteran defender and captain Carles Puyol and midfielder Xavi Hernandez, who will each sign up to stay until 2016.
Puyol, 34, agreed to extend his contract when it expires next year and Xavi, 32, will do so when his expires in 2014.
"This news means that FC Barcelona has secured its ties with three of its most important players," the club said in its statement.
Barcelona are 13 points clear of their fierce rivals, title holders Real Madrid, at the top of the Spanish league, and nine points ahead of second-placed Atletico Madrid, who they beat 4-1 last weekend.
Messi - who has been at the club since 2004 - is the top scorer in the league with 25 goals so far this season and recently broke Gerd Mueller's 40-year record for the most goals in a calendar year.
Mueller scored 85 in 1972 and Messi has scored 90 so far this year, though there are claims that Godfrey Chitalu of Zambia and Zico of Brazil netted more.