He eventually regained control as the game moved into extra-time but, in a World Cup that has seen some outstanding officiating, Geiger's performance - and that of his assistants and the VAR team - left much to be desired.
Pickford's incredible one-handed save looked to put Southgate's men through only for Yerry Mina to jump high at a corner to head home three minutes into stoppage time.
Henderson, meanwhile, had a dramatic evening with the Liverpool midfielder involved in a first-half incident with Wilmar Barrios in which the Colombian escaped a red card despite a headbutt.
England took the lead in a scrappy match when Harry Kane scored from the penalty spot in the 57th minute.
"We do a lot of bonding stuff to really get to know each other and I think that's important as a team off the pitch, to get to know each other".
"This was a game we wanted to win but the knockout is the biggest game for a decade for us and we had to make sure our key players were preserved", Southgate said, via The Guardian, after England's 1-0 loss.
Cavani sends Uruguay to World Cup last eight as Portugal bow out
Portugal finished second in Group B after a thrilling draw with Spain, a slim victory over Morocco and a draw with Iran. This is a side with excellent, Italian-based midfielders in Rodrigo Bentancur, Lucas Torreira and Matias Vecino.
Both Colombia and England are a threat from dead-ball situations.
Yet Colombia did not learn their lesson as Carlos Sanchez, once of Aston Villa, was penalised for dragging Kane to the floor at an England corner.
England have a traditionally poor record with penalties - they were the team's undoing at the 1990, 1998 and 2006 World Cup, as well as the 1996, 2004 and 2012 European Championship.
Colombia came into the game having topped Group H after a disappointing start meant they lost to Japan, but they bounced back defeating Poland and Senegal.
"A player fakes a foul, they are trying to get the referee to book another player", he said.
Expected Crowd Turnout: With its last hosting in this FIFA World Cup 208, Spartak Stadium is expected to be a jam-packed affair, as Colombia meet England, with a total crowd attendance of 44,800.
During the shootout, England goalkeeper Jordan Pickford saved from AC Milan forward Carlos Bacca before Dier stepped up to clinch victory, driving his shot low under David Ospina. At one stage, amid concerns over safety, it seemed many of them might not come.
On paper, England's tilt with Colombia at Moscow's intimate Spartak Stadium is more or less a wash - England is 12th in the Federation Internationale de Football Association rankings and Colombia is 16th, not that the rankings have meant much in an upset-heavy World Cup that's already seen Germany, Portugal, Argentina and Spain eliminated.