There was also concern for defender Alex Greenwood who had to be taken off on a stretcher in the first half after receiving lengthy treatment for a head injury.
The Lionesses went behind after nine minutes after Laura de Neve curled in a superb free-kick.
England managed to go ahead through goals from Lucy Bronze and Fran Kirby but a calm finish from Belgium forward Tessa Wullaert just before half-time saw the two sides level at the break.
Mary Earps - who came fifth in the Ballon d'Or awards on Monday evening - thwarted several attempts from the home side in the second half but could do little about Belgium's third, an 85th-minute penalty cooly converted by Wullaert after Georgia Stanway was penalised for a handball in the box.
England - who must top their Women's Nations League group to qualify for the 2024 Olympic Games on behalf of Team GB - now have two massive fixtures ahead against the Netherlands and Scotland in December.
However, if Belgium were to win their next two games then there is nothing England can do.
Speaking to ITV after the game, Lucy Bronze said she believes they can still get the results required: "We've still got a good chance, we play in our next game against Holland at Wembley - a stadium where we like to step up, against a team that we played quite recently.
"We'll put this game to bed, analyse the game properly and look forward to playing Holland and Scotland. Two really tough games.
"We've left ourselves with a little bit more to do but it's not impossible."
Manager Sarina Wiegman felt the Lionesses had been sloppy on the ball at times.
"They scored three goals and we scored two," Wiegman told ITV after the defeat.
"This was a game I think we should have been tighter on the ball. The tempo wasn't great.
"We did create lots of chances, we dominated the game totally. We lost the ball and they were gone on the counterattack. It was us that made it hard.
"They played top and played very compact. It's something we have to get out of our game. We have to do better in the final third.
"We were sloppy on the ball and they were ready for that. They play their long ball and they are gone. We didn't do it good enough today."
