In a clash between two sides who competed in last season's UEFA Champions League, Ibrahim Maza opened the scoring inside the opening minute, smashing a 25-yard strike beyond Lukáš Horníček.
Yoane Wissa came close to his third goal of pre-season in the seventh minute when he found Mason Miley, who deftly returned the ball into the path of the DR Congo forward, but Wissa's first-time shot was well kept out by Mark Flekken, his former Brentford teammate.
Midway through the first half, Newcastle changed from black and white to their new powder plum third shirt due to a colour clash with Bayer's pale blue strip.
In the 31st minute, Anthony Elanga shot from range but it was too close to Flekken, then Lewis Hall sent a free kick over the bar.
But just before the break, Malick Thiaw - again wearing the captain's armband - headed his side back into the game in towering fashion from a deep Elanga flag-kick from the left.
At the beginning of the second half, Afonso Moreira flashed an effort across goal for the visitors, then in the 57th minute Wissa broke strongly and played the ball out to Nick Woltemade, but the German's low shot was held.
Moreira curled just wide after drifting into the box with a jinking run but with less than eight minutes of normal time remaining, Nigerian striker Boniface zipped home moments after coming on as a substitute.
Harvey Barnes came within a whisker of a late leveller before Horníček pushed away a Patrick Schik shot in a match most notable for Lewis Miley making his return from a fractured fibula and starting alongside his younger brother, Mason, for the first time at senior level.
Newcastle United: Lukáš Horníček, Lewis Hall, Sven Botman, Yoane Wissa, Harvey Barnes, Malick Thiaw (c), Sean Steur, Anthony Elanga, Nick Woltemade (Sean Neave 86), Lewis Miley (Rory Finneran 46), Mason Miley (Miodrag Pivaš 81)
Substitutes: Aidan Harris, Dylan Charlton, Trevan Sanusi, Henry Johnson




