German newspaper Bild quoted Vasco president Roberto Dinamite, who conceded that the 23-year-old is determined to leave.
"I've spoken to the people involved and the situation is irreversible," said Dinamite. "Fagner has made a decision and we have to respect his wishes."
According to Bild, Fagner has already departed for Germany to finalise the deal, reported to be worth €4 million (£3.1 million).
The transfer would make him Wolfsburg's second Brazilian signing of the pre-season after Naldo arrived from Bundesliga rivals Werder Bremen.
Fagner began his career with Corinthians in 2006 and has already attempted the move to Europe, joining Eredivisie club PSV Eindhoven in 2007 only to spend the season stuck at reserve level before returning home with Vasco.