There were no finals berths at stake since Brazil, who have qualified for South Africa 2010, remained top of the South American group on goal difference from Paraguay. Bolivia were already eliminated.
Bolivia went ahead after 10 minutes when midfielder Edgar Olivares headed home unchallenged at a corner.
They doubled their lead on the half hour with a fine free kick by striker Marcelo Martins, who curled the ball over a wall of tall Brazilian defenders and past the static Julio Cesar.
Daniel Alves, being tried out by Dunga in midfield, almost pulled one back with a drive from outside the box in the 36th minute that came back off the post. Striker Adriano went for the rebound but scuffed his shot wide.
The Brazilians pulled one back 21 minutes from time with a typical Dunga style counter-attack that had right back Maicon at its heart.
He robbed the ball in the Brazil box, passed out right to Ramires and charged into Bolivian territory where he picked up the midfielder's ball forward and crossed from the right wing for Nilmar to head in.
Brazil are at home to Venezuela, who are all but out of the running for the finals, in their final qualifier on Wednesday.
Bolivia close their campaign in a match between the bottom two against Peru in Lima on Wednesday. Bolivia have 15 points to Peru's 10.
