Koubek's team ended bottom of Group A with one point following losses to co-hosts Mexico and South Korea and a 1-1 draw with South Africa.
The Czech Football Association announced the news on Monday after the team made their return home from the global showpiece.
The 74-year-old former Viktoria Plzen and Slavia Prague coach was appointed Czechia head coach prior to their play-offs, and they went on to beat the Republic of Ireland and Denmark on penalties to secure their first World Cup spot in 20 years.
FACR supremo David Trunda said in a statement: "We have agreed with coach Miroslav Koubek on terminating our cooperation.
"At a meeting today, the coach offered his resignation and I decided to accept the offer after an open and correct debate.
"Qualifying for the World Cup was an extraordinary moment for all of Czech football, and Mr. Miroslav Koubek played a huge part in it. For that, he deserves my sincere respect and thanks."
The coach added: "After the failure at the World Championship, for which I bear joint responsibility as head coach, after considering all the circumstances, I came to the conclusion that I would offer my position to the President of the FACR, David Trunda.
"After mutual discussion and consultation, the president accepted my proposal. The consequence is the termination of my work with the national team."
The coach further explained his reasoning behind terminating his position.
"A media campaign based on a series of half-truths and fabrications against me also contributed to my decision. In this atmosphere, my work with the Czech national team would no longer make sense," he said.
“I regret that after gaining knowledge from the World Cup, I will not be able to fulfil the specific and clear visions I had for my further work with the national team.”
South Africa head coach Hugo Broos has claimed that whoever succeeds him in his role will have a strong squad to utilise ahead of his imminent departure following the World Cup campaign.
Mexico were impressive in their 2-0 victory over South American rivals Ecuador in their FIFA World Cup Round of 32 clash in Mexico City on Tuesday night.
Mamelodi Sundowns wingback Aubrey Modiba expressed that he would like Hugo Broos to continue as Bafana Bafana head coach after their Round of 32 loss to Canada.
Mamelodi Sundowns star Teboho Mokoena opened up on the emotions felt in South Africa's dressing room after their FIFA World Cup 2026 Round of 32 loss against Canada.
