30-year-old Czech Republic debutant Zdenek Ondrasek scored a late winner as England suffered their first qualifying defeat for a decade, as Gareth Southgate’s side is made to wait to secure their place at Euro 2020.
The Three Lions went ahead from the penalty spot inside five minutes through captain Harry Kane, before Jakub Brabec put the hosts back on level terms just four minutes later.
After equalising, the Czech Republic grew into the game creating the majority of chances and stifling a lacklustre England.
Jordan Pickford was called into action to deny Lukas Masopust and Alex Kral as the home side continued to dominate, before Ondrasek swept home winner with five minutes remaining.
The win sees the Czech Republic move level on 12 points with England in Group A, while also handing them a first defeat in qualifying in a decade.
England last lost a qualifier against Ukraine in October 2009 and had won all four games so far for Euro 2020 qualification. They can still progress to next year's tournament with victory over Bulgaria on Monday.
Mason Mount was handed his full England debut as Gareth Southgate made three changes ahead of kick-off. Danny Rose and Kieran Trippier came in at full-back in place of Trent Alexander-Arnold and Ben Chilwell from the Three Lions’ 5-3 win over Kosovo.
England got off to the perfect start and were awarded a penalty in the fourth minute when Raheem Sterling burst into the box, cut inside Masopust and was brought down by the defender.
Kane stepped up and converted from the spot, calmly passing the ball straight down the middle with goalkeeper Tomas Vaclik going the wrong way.
The home side restored parity just four minutes later. A swift response finished off after a corner was flicked on and Jakub Brabec was left unmarked at the back post to apply the simple finish.
There were question marks over England’s defending before the match and they started poorly in Prague once again. The Czech Republic had a chance to go in front themselves following another corner but Patrik Schick couldn’t direct his header on target.
After a fast and furious opening the game slowed dramatically as both sides struggled to create any clear cut chances. England were stifled, frustrated and lacked fluidity as the game went into the break at 1-1.
There were no substitutions for Gareth Southgate’s side but he opted for a change of system after the restart playing 4-3-3 in a bid to get things going.
It was the Czech Republic who had the first real chance of the half though. After Harry Maguire gave the ball away, Tomas Soucek fired high and wide from the edge of the area in plenty of space.
Sterling finally managed to get in behind the back four once again after a well weighted ball from Kane. The City forward tried to round Vaclik but he did really well to get down, get a hand on it and palm it away to safety.
Masopust almost made amends for giving away the early penalty, forcing Jordan Pickford into a decent save. The right back cut inside and sent a dipping left-footed effort towards goal from 20-yards out and the Everton keeper tipped it over the crossbar.
Pickford was called into action once agin with just over ten minutes to go. This time denying Alex Kral’s powerful strike that was sneaking in at the near post.
A fairy-tale moment for Zdenek Ondrasek, who came on as a substitute for his Czech Republic debut at the age of 30, as he marked that with what would be the winning goal of the game, sweeping home from six yards out.
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