The Southampton midfielder struck a superb set-piece goal but it wasn't enough for the Three Lions as individual errors led to their downfall in Southern France
Poor hands from Jack Butland allowed Alisson to give the South Americans an early lead, and they were able to double that lead when Lucas Silva took advantage of a slip by Liam Moore in the Three Lions defence.
Ward-Prowse did pull one back nine minutes from full-time, but England must now beat South Korea to keep their chances of reaching the final alive, though a place in the play-off for third place now seems much more likely.
Manager Gareth Southgate made five changes from England's opening 3-0 win over Qatar as the likes of captain Butland and Nathan Redmond returned after being rested against the Middle Eastern outfit, but the former Middlesbrough boss will not have been happy with the way his side began the match.
The Selecao were able to impose themselves in possession, and were able to take a deserved lead inside nine minutes.
Alisson drove into the box but the chance seemed to have gone when Butland came off his line to smother, only for the ball to slip from his grasp and leave the Brazil striker with a tap-in from inside the six-yard box.
That did at least wake the Three Lions from their slumber, and Saido Berahino almost tested Marcos as he beat Marquinhos to a ball over the top, but the Paris Saint-Germain defender recovered well to clear the danger.
England did eventually work the goalkeeper as Redmond find space on the left before cutting inside on the edge of the area, and teenager Marcos did well to tip the low effort around the post.
The remainder of the first half passed without incident, though England did begin to enjoy periods of possession that forced the Brazil defence into depeer areas.
The second half began in similar fashion, and so it was disappointing that an individual error led to Brazil's second goal.
Thalles' ball into Lucas Silva took a bobble off the pitch as Moore looked to clear, and the midfielder had the relatively simple task of running the ball to the edge of the area and angling an effort past Butland into the bottom corner.
England introduced Cauley Woodrow and Brad Smith off the bench, and it was the latter who helped the Three Lions back into the game.
The Liverpool left-back broke forward after Nathaniel Chalobah did well in midfield, and he was able to win a free-kick as Gilberto handled right on the corner of the area.
Ward-Prowse stepped up to strike the set-piece, and his wonderful curling effort evaded Marcos as it nestled in the top corner.
That was as good is at got for England, though, as the the tournament favourites were able to hold out for the final ten minutes to all but secure their place in Sunday's final.