The German referee awarded a pair of questionable penalties - one to each side - that VAR official Christian Dingert surprisingly confirmed upon review.
Lyon, who carried a 1-0 aggregate lead into the second leg of the last-16 tie, scored first after Houssem Aouar was judged to have been fouled inside the area, despite replays showing that Rodrigo Bentancur clearly tackled the ball when sliding for his challenge.
Memphis Depay took advantage with a Panenka to score a priceless away goal.
Not to be outdone, Juve were given their own chance from 12 yards out when Depay apparently handled a Miralem Pjanic free-kick, even though his arm was tucked well into his body in the wall.
Cristiano Ronaldo leveled the proceedings with the ensuing spot-kick.
If nothing else, at least Zwayer was consistent?