Suffering their first defeat at Wembley in 21 matches since losing to Denmark by the same scoreline in October 2020, Gareth Southgate's men packed little punch attacking-wise and succumbed to Endrick's record-breaking goal in the 80th minute.
The 17-year-old's tap-in saw him become the youngest-ever player to score a senior goal for club or country at Wembley, where Brazil were fortunate not to receive greater punishment for a series of fouls, but England's mediocre offensive display did not merit much either way.
Newcastle United winger Anthony Gordon was selected on the left for his Three Lions debut at Wembley, where Ollie Watkins and Conor Gallagher were also given the nod up front and in midfield respectively.
Meanwhile, both of Brazil's centre-backs - Fabricio Bruno and Lucas Beraldo - made their senior Selecao debuts alongside goalkeeper Bento, but it was the visitors who made the man in between the sticks work early doors.
Rodrygo let fly from range in the ninth minute, but Jordan Pickford got down low and saved without too much difficulty, although he was beaten by a tame Vinicius Junior strike in the 12th minute and was indebted to Kyle Walker for bursting back and stopping the ball en route to goal.
However, the Manchester City right-back - donning the captain's armband for England - then succumbed to an apparent hamstring injury in the 19th minute, one moment before Bruno hit the ball onto Watkins's outstretched leg from close range and breathed a sigh of relief as the Aston Villa striker's 'effort' flew over the top.
Walker's withdrawal allowed Ezri Konsa to come on for his senior debut at right-back, where he would be assigned the daunting task of trying to contain Vinicius Junior, and the gilt-edged chances continued to come Brazil's way.
With 10 minutes of normal time remaining in the first half, Lucas Paqueta wasted a magnificent chance from inside the box - striking the post with a first-time effort - before Raphinha failed to punish Harry Maguire for a defensive blunder in the 42nd minute, firing wide after the Manchester United man had gifted him possession.
England's display was far from disastrous, but a succession of fouls from Dorival Junior's men prevented the Three Lions from entering top gear - Paqueta in particular was living a charmed life after already entering the referee's book.
Southgate's men were asking questions of the Brazil backline from set-pieces, though, as a 50th-minute Declan Rice free kick to the back post was on the money for Gordon, but Bento managed to parry his first-time effort to safety.
With the contest going stale, Paqueta - arguably fortunate to still be on the field - very nearly provided a moment of magic in the 63rd minute, trying to pick out the top corner with a first-time 20-yard strike and only missing by a few centimetres.
Having effectively been marked - and fouled - out of the game, a miffed Bellingham was substituted midway through the second half, before another couple of changes saw 18-year-old Kobbie Mainoo brought on for a dream Three Lions debut.
However, it was one of Brazil's fledgling midfielders who would let out an almighty roar of elation in the 80th minute, where a poor Lewis Dunk header fell at the feet of Andreas Pereira, who sent Vinicius away.
Pickford came out on top in his one-on-one with the Real Madrid winger, but the rebound fell for Endrick, who had kept up with his compatriot, held his run behind the ball and tapped the rebound into an empty net.
An incessant England were adamant that either Vinicius or Endrick were offside in the build-up, but the latter's goal stood after a VAR check, and the 17-year-old should have doubled the Selecao's advantage right at the death following a counter-attack, only to shoot straight at Pickford.
England now seek a response when Belgium pay a visit to Wembley on Tuesday, while Dorival Junior - who also ended the visitors' three-game losing run on his baptism - bids to make it two for two in the Brazil hotseat against Spain in three days time.