De Ligt was given his marching orders in the 55th minute for a deliberate handball on the last line of defence, with Netherlands boss Frank de Boer claiming it changed the game.
The Czech Republic took the lead on 68 minutes when Tomas Holes netted, before the Slavia Prague man set up Patrik Schick to seal the win in the 80th minute.
I thought we were in control,” de Boer said post-game. “In such a match it is only about one or two moments.
“(Donyell) Malen got it. And shortly after that you are with ten men. Then it becomes difficult.
“You hope that they become frustrated and take risks so that you get more opportunities yourself. Then you dont have to find out, no. Then they can play their own game.”
PSV Eindhoven talent Malen, who got in behind the Czech defence but spurned his chance shortly prior to the red card, was replaced by Quincy Promes not Wout Weghorst two minutes after de Ligt’s red card.
“Donyell is a very explosive player who is taxed after 60 minutes in these kinds of games,” de Boer explained.
“My plan was to bring in Weghorst for Donyell, but when we started playing 4-4-1 you need someone who is on the line. Can go up and down and stand his ground defensively.”
The Czech Republic advances to the quarter-finals where they will face Denmark in Baku.