After lengthy protests, Sanchez eventually left the field and Kagawa was allowed to slot the penalty clinically into the bottom right corner of the net and Colombia's game plan was in tatters.
And Japan made them pay as Shinji Kagawa finished the penalty kick with class for the 1-0 lead.
Not only was Osako instrumental in both goals, he sprawled to block a close-range shot by Colombia midfielder James Rodriguez in the waning minutes.
Slovenian referee Damir Skomina flashed a straight red card for Carlos Sanchez after he blocked a Shinji Kagawa's shot with his arms.
Colombia equalised six minutes before the interval when Juan Quintero's low free kick squeezed over the line.
Judge sends President's aide to jail
The order marked the latest fall for the political power broker and confidant of Republican presidents dating to Ronald Reagan. Asked whether he might consider pardoning former aides and advisers, Trump answered, "I don't want to talk about that".
Pekerman defended his strategy, which included subbing in attacking midfielder and 2014 Golden Boot victor James Rodriguez, who had been left out of the starting lineup because of muscle pain.
It took 18 attempts, but finally an Asian team have triumphed over the perennial World Cup achievers of South America, with the former continent suffering 14 defeats during that time.
His sending-off in the third minute, for a deliberate handball, was the second fastest in World Cup history after Uruguay's Jose Batista was dismissed after 55 seconds against Scotland in 1986.
"I told them at halftime to keep moving, get the advantage in positioning", Japan coach Akira Nishino said.
After the break, Japan pressed a exhausted Colombia side and Yuya Osako grabbed the victor with a glancing header in the 73rd minute.
Colombia got off to a disastrous start when an error by Davinson Sanchez saw Osaka break through on goal.
Argentina reveal Sergio Aguero will start over Gonzalo Higuain vs. Iceland
From a football perspective, there is nothing not to love about the least populous nation ever to play in a World Cup. Guerrero has said the failed drug test came from tea served in a cup tainted with coca leaf residue in a Lima hotel.
The complexion of the game in Saransk was changed radically when Colombia's Carlos Sanchez was shown the first red card of Russian Federation 2018 for handball in the opening minutes of the contest.
He came on to join captain Radamel Falcao in the 59th minute, but his best chances were thwarted by Japan's desperate defending near the goal.
Japan upset 10-man Colombia 2-1 in a dramatic match on Tuesday to become the first Asian side to beat South American opponents at the World Cup.
Colombia responded well to going a goal and a man down, but when, in the second half, they could barely get a touch of the ball, Pekerman brought on James Rodriguez.
California three-state plan faces major legal, political hurdles
Though it isn't likely to get voter approval, it would still have to clear numerous hurdles, including getting approval from U.S. It would be the first division of an existing US state since the creation of West Virginia in 1863.