With Colombia already through to the knockout stage, Mondragon, who celebrated his 43rd birthday last Saturday, replaced first-choice David Ospina for the Group C match in Cuiaba.
His appearance broke a record previously held by Cameroon striker Roger Milla, who played -- and scored -- at the age of 42 years and 39 days in a 6-1 defeat against Russia in 1994 in the United States.
"Faryd has been a very important player for us," Colombia coach Jose Pekerman said after Colombia beat Japan 4-1. "His performance was good and we always knew that our goal was well protected with him.
"When you have a national team, you have to protect your players. He has experience and other players are young, so he can share his experiences with them. We gave him a chance to play today so he can be recorded as the oldest goalie in the World Cup."
Mondragon took time to reflect at the end of the match.
"It's a great moment, at the end of a long journey, to play at the age of 43 at the World Cup, he said. "Thanks to all my colleagues.''
Mondragon jogged onto the pitch to a thunderous ovation from the large pro-Colombian crowd, and left it with the match ball under his arm.
"That's for my own private museum," Mondragon said with a smile.
Mondragon was a non-playing member of Colombia's 1994 World Cup squad -- whose group-stage elimination was followed by tragedy when captain Andres Escobar was shot dead in a Medellin nightclub car park less than two weeks after scoring an own goal against the United States.
Mondragon appeared in all three of Colombia's matches at the 1998 tournament in France, notably excelling with a series of fine saves in a 2-0 defeat against England in Lens.
He has taken part in six qualifying campaigns during a 24-year career that has seen him play for 11 clubs in eight countries.
Mondragon began his career in 1990 with Colombian side Deportivo Cali, where he has also played for the last two years following spells in Paraguay, Argentina, Spain, France, Turkey, Germany and the United States.
A short spell in France's Ligue 1 with Metz was cut short by the legal system in April 2001 when he was found guilty of using a fake Greek passport to secure the move. Mondragon was banned from entering France for two years and fined 30,000 pounds by a Paris court.
However, he remained in Europe for another nine years, playing in Turkey for Galatasaray between 2001 and 2007 and winning two league titles in the process, before moving to Germany with FC Koln.
He then moved to Philadephia Union in Major League Soccer for the 2011 season before returning to Colombia to rejoin his first club, Deportivo Cali.