De Boer faced fierce criticism after the loss to the Czechs because of his decision to abandon the traditional Dutch formation of four defenders, three midfielders and three forwards.
Criticism of Frank de Boer's decision to play a formation of three defenders, five midfielders and two forwards that had been largely silenced by the victories returned after the loss in Budapest.
With De Boer dealing with injury problems and a dearth of top-class wingers to succeed Arjen Robben, he opted to ditch the once-sacred 4-3-3 formation and switch to a 3-5-2.
In their first major tournament since the 2014 World Cup, the Dutch now know they will play one of the best third-placed teams in Budapest in the last 16 on June 27.
"I had to leave the room," said coach Frank de Boer, who coached Eriksen at Ajax earlier in the midfielder's career.
De Ligt is recovering from a groin injury but has been training with the team in recent days.
Crystal Palace manager Frank de Boer vows to fight on, Newcastle counterpart Rafael Benitez gets boost
Frank de Boer vowed to fight for his future after a 1-0 defeat at Burnley piled pressure on the Crystal Palace manager.
Chris Wood marked his maiden appearance for Burnley at Turf Moor by firing the winner early in the first half.
De Boer took the helm at Selhurst Park forward following Sam Allardyce's unexpected departure at the end of last season.