The City centre-half, who spent the 2021/22 campaign on loan firstly at Belgian side Anderlecht and more latterly Stoke City, was a commanding figure at the heart of Lee Carsley’s side in České Budějovice.
An early first-half strike from Arsenal’s Emile Smith-Rowe, who expertly despatched a 22nd minute half volley, sent England in at the break armed with a crucial lead.
And England doubled their tally just 47 seconds after the restart when Aston Villa’s Jacob Ramsey slotted home from close range after great work from Morgan Gibbs-White.
However, Czech substitute Daniel Fila fired in a stunning 88th minute 25-yard shot to set up a nervy finish but England held firm to secure all three points.
The victory saw the Young Lions leapfrog the Czechs into top spot in Group G and served as a huge boost for their hopes of qualifying for next summer’s showpiece to be held in Romania and Georgia.
Carsley’s side are on 19 points but have three games left to play – the Czechs also have 19 but with an inferior goal difference and have only one match outstanding.
It means four more points will seal England's qualification.
Only the leaders are guaranteed to qualify for the finals with one spot also available for the best runners-up.
England are next in action on Tuesday when they play host to Albania’s Under-21s at Chesterfield, kick-off 7.45pm.