The 17-year-old opened the scoring for his side in the 34th minute just before Grant-Leon Mamedova extended his side’s lead in the 49th minute of the first half.
David Hummel’s brace in the 58th and 70th minutes respectively restored purity for Stuttgart to level the game.
The Brikama-born player who was signed from Hoffenheim’s youth setup has now scored three goals in succession for Bayern U-19 so far.
Sanyang, who arrived in Germany at the age of ten as a refugee, played 19 games for Hoffenheim U-17, scoring eight goals and assisting four before joining Bayern.
The latest result has leveled both teams (Bayern and Stuttgart) on each seven points but Bayern lead on goal difference after playing three games.