Brazil's victory margin could have been greater, but Luis Fabiano missed a penalty after Foster fouled Nilmar.
England battled hard against a superior Brazil, but Nilmar headed Elano's pass beyond Ben Foster after 47 minutes.
Striker Nilmar scored a hat-trick to lead already-qualified Brazil to a ninth victory in the South American qualifying group.
Brown made amends for his earlier error with 14 minutes left by crucially blocking Nilmar's header after Brazil caught England on the break.
Former Manchester City midfield man Elano split Wes Brown and Matthew Upson with a glorious pass and Nilmar arrived to direct a header beyond Foster.
Spain's Villarreal edged out Bulgarian visitors Levski Sofia with a 1-0 victory as striker Nilmar added to his recent hat-trick for Brazil with a 72nd-minute winner after good play out wide by substitute Giuseppe Rossi.
To this end, Brazil rested Robinho, bringing in Nilmar up front to partner Luis Fabiano, who scored a hat-trick in that 6-2 win and bagged a brace in their previous group game against the Ivory Coast.
England should have fallen further behind a minute later when Brown's attempt to chest the ball back to Foster only let in Nilmar, who was hauled to the ground by Foster as he went around the England keeper.
Unsurprisingly, the already qualified Brazil were the more positive of the two sides but were only able to fashion a handful of chances, the best of which fell to striker Nilmar but was superbly saved by goalkeeper Eduardo.
They combined on the half hour with Fabiano crossing for Nilmar at the back post, who looked certain to score only for Eduardo to produce a superb point blank save to push the ball on to the post and deny him.
Portuguese keeper Eduardo was the chief reason for denying Brazil when they did break forward, brilliantly tipping Nilmar's close-range effort onto the post in the first half before clawing the ball away from his top corner from Ramires' deflected strike late on.
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