Fabio Capello's side fell victim to a goal early in the second period from Nilmar to leave England still without a win in eight matches on neutral territory against the Brazilians.
Fabiano also missed a penalty for Brazil, who unsurprisingly dominated possession.
They were aided by an England midfield which gave the ball away far too easily and consequently the front two of Rooney and Darren Bent were starved of any worthwhile service.
But this was no vintage performance by Brazil and their trickery was largely confined to in front of the back four and goalkeeper Ben Foster, apart from an impressive spell after the break.
Capello will now have four months to reflect on how many of his fringe players pushed their claims to be part of his World Cup plans before the next international in early March.
Only Aston Villa winger James Milner, who was making his full debut, could feel he furthered his cause on the left wing to any significant effect.
Capello's squad had already been decimated by the absence of David James, Glen Johnson, Rio Ferdinand, Ashley Cole, Steven Gerrard, Frank Lampard, David Beckham, Aaron Lennon, Theo Walcott and Emile Heskey.
But he was forced to further reorganise when skipper John Terry lost his battle to recover from an Achilles problem and midfielder Michael Carrick was ruled out with an ankle injury.
It meant Gareth Barry and Rooney were the only first-choice players in the starting XI, in contrast to Brazil who were virtually at full strength.
Capello handed a first start since his opening game in charge against Switzerland to Jermaine Jenas and there were only three survivors from the starting XI against Belarus last month in Foster, Wayne Bridge and Barry.
It was a similar scenario to 12 months ago when a scratch side won 2-1 against Germany in Berlin but Brazil unsurprisingly provided a sterner test given that they have regained the number one spot in the FIFA world rankings.
Players from both teams paid their respects to German goalkeeper Robert Enke, who died earlier this week at the age of 32, before kick-off during a period of silence.
England began promisingly and a low cross from Shaun Wright-Phillips just eluded the run of Rooney into the Brazilian box, but Dunga's side were soon in control and knocking the ball around in confident style.
A mistake by Matthew Upson allowed Nilmar to cut in unopposed from the left flank but his low centre was intercepted by Bridge.
Kaka showed his class and determination in shaking off challenges from Barry and Jenas before attempting to release Fabiano but Bridge was alert to the situation.
Felipe Melo got the better of a tussle with Upson but overran the ball and Foster was able to hack clear, albeit in unconvincing fashion.
Kaka was pulling the strings and the Real Madrid star picked out the overlapping Michel Bastos whose cross-cum-shot fizzed just past Foster's left hand post.
Melo then showed neat skill to create space for himself on the edge of the box but his shot sailed straight at Foster.
Kaka forced Foster to save away to his left with an angled drive after linking up well again with Fabiano as the half ended goalless.
But it needed only 90 seconds of the second half for Brazil to break the deadlock through Nilmar.
Elano's dipping cross picked out the run of Nilmar, who got in between Lescott and Upson before arrowing his header past the dive of Foster into the corner of the net.
Bent had little opportunity to impress before he was substituted after 54 minutes and replaced by Jermain Defoe.
A minute later Brazil had a golden chance to double their lead when goalscorer Nilmar was brought down in the area by Foster after Wes Brown had attempted to chest the ball back to him.
Foster was shown a yellow card but England were given a reprieve when Fabiano sent his spot-kick high over the crossbar.
There was little to enthuse about in a low-key finale to the game as both teams made several substitutions, although Lucio crashed a shot against the post.
There was time for Capello to bring on Tottenham midfielder Tom Huddlestone, who replaced Barry.