Led by Pinto, Costa Rica were the Cinderella story of the World Cup in Brazil as the CONCACAF representatives reached the quarter-finals for the first time in their history.
But the 61-year-old - in his second stint in charge of the national team - will not continue in his role after he was unable to come to terms on a new contract with the Costa Rican Football Federation (Fedefutbol), who confirmed the news on Thursday.
A factor behind the Colombian-born tactician's decision to step down was Fedefutol's refusal to allow him to choose his backroom staff.
"I realised I would not be able to count on conditions to carry out my work," Pinto said on his own personal website.
"So it wasn't possible to reach an agreement (to renew my contract)."
Fedefutbol president Eduardo Li said the search was underway for a replacement but kept the door open for Pinto and a possible return to the helm.
"I thank heartily Pinto. Entire Costa Rican people, coaches and managers are pleased with what was achieved in just Brazil 2014," said Li.
"Unfortunately we were unable to agree on some aspects. Doors are open, do not rule out in the future to have the opportunity to have Pinto back."
After initially coaching Costa Rica in an unsuccessful spell between 2004 and 2005, Pinto returned to the hot seat six years later and guided the Central American nation to World Cup qualification.
At the showpiece event, Pinto's men defied all odds to top Group D undefeated ahead of powerhouse opponents Uruguay, Italy and England and book their spot in the last-16.
In the first knockout round, Costa Rica overcame 2004 European champions Greece on penalties after playing an hour with 10 men before they were bundled out in the quarters by the Netherlands, who prevailed in a shoot-out.
