Playing for the first time since Sunday's qualifier against Argentina was controversially suspended mid-game, Selecao netted twice in a lively first half to set up the win.
Brazil's opener came in the 14th minute when Neymar laid off for Everton Ribeiro, who scored the winner in last week's 1-0 triumph in Chile.
Neymar grabbed the second goal five minutes before the break, the Paris Saint-Germain star tapping home from close range as Brazil made it eight wins from eight games on the road to Qatar 2022.
On a night when Argentina's Lionel Messi overtook Pele as the leading goalscorer in South American history with a hat-trick, Neymar's strike took him to 69 for Brazil, moving within eight of the Brazil great.
Both sides had early chances in a lively opening, with Gabriel 'Gabigol' Barbosa having an effort blocked while Gianluca Lapadula shot over for Peru.
Peru goalkeeper Pedro Gallese made a strong save with his left arm as Gerson broke forward, firing on target on his left.
Brazil broke the deadlock in controversial circumstances after Neymar bundled over Anderson Santamaria and raced down the byline to centre for in-form team-mate Ribeiro to side-foot home – Peru's protests fell on deaf ears.
Lucas Paqueta almost doubled Brazil's advantage with a 34th-minute chance, before Neymar scored Selecao's second goal six minutes later.
Danilo passed for Gabigol, whose cutback fell to Ribeiro. The Flamengo midfielder's shot was blocked into Neymar's path for a point-blank finish.
Peru substitute Gabriel Costa's 72nd-minute cross-cum-shot tested Brazil goalkeeper Everton as the depleted hosts, missing several key players unable who were not released by their Premier League clubs, seemed content with the victory.
Veteran Brazil substitute Hulk rounded Gallese late but blasted wide on his preferred left foot.