Neymar suffered an adductor muscle injury while taking a shot and was replaced by Everton's Richarlison.
And the Toffees forward proved to be the match-winner, powering home a header on the stroke of half-time.
Manchester City's Gabriel Jesus struck the post for Brazil in the second half, while Arthur hit the crossbar with a long-range effort.
The 29,669 fans at Stadium MK cheered loudly when Neymar came out to warm-up, but were equally displeased when he hobbled off.
Brazil team doctor Rodrigo Lasmar said: "He felt discomfort. He will need a bit more time to evaluate it and take a scan, but in principle it is not a serious injury."
Elsewhere, his fellow PSG forward Kylian Mbappe went off with a shoulder injury during France's friendly against Uruguay.
The French champions' next match is at home to Toulouse on Saturday.