As the half wore on, Los Cafeteros began to grow in confidence and, in the 39th minute, they duly levelled the scores when Quintero cleverly fired a freekick under the Japan wall and Eiji Kawashima was unable to scramble across in time to keep it over the line.
Sanchez will miss Colombia's second group game against Poland. His shot was saved by the out-rushing David Ospina with the rebound from Shinji Kagawa apparently blocked by the hand of Carlos Sanchez. Falcao captain's Colombia in his first World Cup appearance.
Yuya Osako's 73rd-minute victor was a huge relief for the Japanese, who were thumped 4-1 by Colombia four years ago during a miserable campaign in which they failed to register a single win.
Colombia defender Carlos Sanchez Moreno has received the first red card of World Cup 2018 in Russian Federation.
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But Japan finally made their extra man count when Osako, who was a constant menace to the Colombia defence, leapt highest from a corner and guided his header in off the post with 17 minutes to go.
That's the second earliest red card in World Cup history, with Uruguay's Jose Batista still holding the record of 54 seconds from back in 1986.
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"I think the Argentinians felt a bit frustrated that they weren't getting through and it was important we equalized so quickly". His most recent World Cup goal was in the same game when he scored a minute into stoppage time to close the first half.
Barrios was booked for a foul on Kagawa, and then Inui threatened again before his shot, after cutting inside, was blocked by a defender.
Victory for the Samurai Blue is their first ever on European soil at the World Cup and their first against South American opposition in the competition.
Japan started the game on an exciting note, pressing heavily from the word go as they had a shot at goal inside the first couple of minutes.
Akira Nishino was only appointed as Japan coach in April, replacing Vahid Halilhodzic during a tumultuous build-up to their World Cup campaign.
Despite the numerical disadvantage, Colombia gained a foothold in the game and were awarded a free-kick on the edge of the area in the 38th minute after Falcao was bundled over by Yoshida.
Colombia started without Rodriguez, the leading scorer at the 2014 World Cup in Brazil.
When the game was due to start, Falcao walked across to Japan's side of the field and spoke to referee Damir Skomina in a discussion that lasted beyond the official countdown to kickoff.