Youri Tielemans and Dries Mertens found the net to keep Belgium top of Group A2.
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Classy first-half strikes by Youri Tielemans and Dries Mertens strengthened Belgium's finals ambitions as England missed out on reaching the final four.
Match in brief
An end-to-end opening period was illuminated by two precise long-range strikes, Tielemans' low drive creeping past Pickford after Belgium had won possession inside the visitors' half.
Romelu Lukaku, who had set Tielemans up, then cleared Harry Kane's header off the line, only for England to fall further behind when Mertens curled in a superb free-kick.
Both sides sporadically threatened during the second half as the hosts saw out the win, ending their opponents' hopes of reaching the final four for a second successive season and giving themselves the chance to win the group by avoiding defeat at home to Denmark on Wednesday.
Dante Bellon, Belgium reporter
What looked like an easy win after the first half, became a tough win after 90 minutes. England pressed Belgium back to their own goal in the second half. Mertens scored in his home town to keep Belgium in the race for the final four. One last hurdle to pass: Denmark on Wednesday.
Simon Hart, England reporter
England's finishing touch was lacking tonight as their UEFA Nations League hopes were extinguished, but there was one considerable silver lining in the performance of Jack Grealish on his first competitive start. The Villa star was the go-to man, always wanting the ball and looking to make things happen, be it by linking up with the forwards or taking on defenders. The fact he suffered more fouls in a match than any England player since Kane against Colombia at Russia 2018 says it all about his threat.
Roberto Martínez, Belgium coach: "It is the perfect present for my 50th game as a head coach for Belgium. We started the game very well but had some difficulties in the second half. Now we have to complete one more hurdle by earning three points in Leuven next Wednesday."
Dries Mertens, Belgium forward: "It's always fun to score goals and it definitely is when it's in your home town. It must have been a long time since I've scored here. I never played for the first team of Leuven, but in the youth team I scored a couple of goals."
Gareth Southgate, England coach: "I think we played pretty well in the first half. There wasn't much between the teams – two moments for Belgium, where we conceded possession and a top quality free-kick. The performance level of the team was very good. If we perform in that way then we'll continue to improve as a team."
Harry Kane, England captain: "Personal milestones are great but it's all about winning games. I thought we probably did enough to win the game today. We were fantastic out there, unlucky to concede the two goals we did. After that we played great football, created a lot of chances. Probably the only thing [was] the final product and the final finish weren't good enough."
• Belgium have scored at least two goals in eight of their last nine UEFA Nations League matches and 19 of their last 20 competitive matches (W18 L2).
• The Red Devils are unbeaten in their last 28 competitive home matches – their last defeat was against Germany in 2010.
• England lost for only the second time in 27 competitive away games (W17), having kept a clean sheet in 17 of those matches.
• Gareth Southgate's side conceded as many goals as they had in nine previous matches.
• Captain Harry Kane made his 50th appearance for his country, narrowly failing to add to his record 25 England goals in games when starting as skipper.
Belgium: Courtois; Meunier Alderweireld, Denayer, Vertonghen; Tielemans, Witsel, T Hazard; Mertens (Praet 83), De Bruyne; R Lukaku
England: Pickford; Mings, Dier, Walker; Trippier (Sancho 70), Rice, J Henderson (Winks 46), Chilwell (Saka 38); Grealish, Mount (Calvert-Lewin 69); Kane
The UEFA Nations League final tournament takes place from 6-10 October 2021. Teams will return to competitive action in the spring in the European Qualifiers for the 2022 FIFA World Cup.