The talismanic striker scored from the spot in the 64th minute in Yokohama, providing Colombia with some crumbs of comfort after they were stunned 2-1 by the Blue Samurai at last year's World Cup in Russia.
Queiroz, who stepped down as Iran boss after eight years in charge following the Asian Cup earlier this year, has inherited a team in transition from former coach Jose Pekerman.
But with Falcao and James Rodriguez available, Colombia still had plenty of firepower in attack among a group of players eager to impress former Real Madrid manager Queiroz.
Sebastian Villa rattled the crossbar in the early skirmishes before Ritsu Doan and Shoya Nakajima went close for Japan, who will take part in this summer's Copa America as guests.
Whatever Queiroz said to his players at half-time worked as Colombia came out with more purpose, Falcao having a goal ruled out for an infringement in the build-up just after the break.
But the Monaco forward stepped up to convert the decisive spot kick after Takehiro Tomiyasu handled inside the box.
Japan threw on veteran playmaker Shinji Kagawa, who made a busy cameo, but were unable to find the equaliser.