The split comes just one year into Sampaoli's five-year contract.
The 58-year-old's days as coach were numbered after his Lionel Messi-led side failed to fire in Russia, their campaign fraught with tension and dispute.
Appointed in June 2017, his final game in charge was the last-16 defeat to France, who were crowned world champions earlier Sunday.
Divorce proceedings were complicated by Sampaoli's reluctance to resign and a costly contract clause were the AFA to sack him.
Reports suggest he walks away with a $2 million pay-off.
Sampaoli's record makes grim reading given Argentina's usually high standards: seven wins, four draws and four defeats in 15 matches.
He was hired with a big reputation after guiding Chile to the 2015 Copa America title -- beating Argentina on penalties in the final.
Sampaoli's team drew the first three qualifiers under his watch but Messi scored a hat-trick in a 3-1 win at Ecuador to send Argentina to Russia.
But things quickly turned sour during the tournament itself as Messi missed a penalty in the opening 1-1 draw with minnows Iceland, followed by a chastening 3-0 defeat to Sunday's beaten finalists Croatia.
A 2-1 win over Nigeria saw them progress as group runners-up to the knock-out stages where they fell 4-3 to France, a defeat that sealed Sampaoli's fate.
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