Chelsea striker and joint top Premier League top scorer Tammy Abraham was only allowed to play two-minutes of regulation time in a match, which England lost and sealed any hopes of him playing for the Super Eagles of Nigeria.
His teammate, Fikayo Tomori, who is also eligible to play for Nigeria sat on the bench throughout the game.
Abraham came in as a substitute for Declan Rice in the 88th minute after The Czech Republic had already wrapped up the game with substitute Zdenek Ondrasekat’s 85th minute winner.
England drew the first blood when Kane converted a penalty in the fifth minute of the game after Lukas Masopust fouled Raheem Sterling.
The lead lasted for less than five minutes as Jakub Brabec equalised following a corner.
England can still qualify on Monday if they beat Bulgaria and Kosovo do not beat Montenegro.