Spain defeated Croatia 4-1 in Seville on Tuesday (Wednesday AEST), with Lamine Yamal starring. The Barcelona teen scored two and made one, for Marc Pubill, before substitute Nico Williams added the late fourth.
England were more tested by the Czech Republic in Prague until Pavel Sulc was given a 26th-minute red card following a VAR review for a late and high tackle on Elliott Anderson.
The Czechs battened down the hatches and saw out the half, but soon after the break Trent Alexander-Arnold, making his first start under Thomas Tuchel, crossed for Anthony Gordon to head in.
Harry Kane, whose missed penalty at 2-1 cost England at the weekend, pounced on a loose ball to drive in his 87th England goal in the 69th minute and the contest was effectively over.
Bournemouth's Alex Scott made his England debut, and Liverpool teen Rio Ngumoha his competitive bow.
"We played very professionally in the second half," England coach Tuchel said.
"We stepped up, we needed to be a bit more dynamic and bring a bit more urgency into our play, which we did, but we kept the intensity going, and the effort was still there. We deserved victory. We got an important win, and that's what counts."
Spain now top Group A3 with six points from their two wins, while Croatia and England, who meet in Rijeka on Saturday (local time), have three points each.
"He is a very generous footballer who puts all that talent at the service of the team," Spain coach Luis de la Fuente said of Yamal.
"We are fortunate to have him with us. He is someone who is truly loved within the squad. We are very happy with him."
In the second-tier Group B1, new Scotland coach Sebastien Pocognoli is still awaiting his first goal after the side's scoreless draw in Slovenia was followed by a 3-0 home loss to Switzerland.
Jack Hendry's 12th-minute red card, given for hauling down Nottingham Forest's Dan Ndoye on the edge of the area, was a bad start for the 39-year-old Belgian coach, and it got worse when veteran Ricardo Rodriguez curled in the subsequent free kick.
In the second period Leeds' Nico Elvedi and Burnley's Zeki Amdouni secured the win, both set up by Ndoye.
In the group's other game, Slovenia beat North Macedonia 2-0 to move into second behind the Swiss.
In Group C1, Finland and Belarus drew 0-0, while Albania won 3-0 in San Marino.
Moldova were held to a 1-1 draw at home to the Faroe Islands, and Slovakia beat Kazakhstan 2-1 in Group C3.
In Group C4, Iceland were 3-0 winners in Luxembourg, and Estonia drew 1-1 in Bulgaria.
The Nations League, a biennial tournament featuring promotion and relegation, and a finals series for League A, also serves as part of qualification for Euro 2028.
- with AP