The Magpies were clearly intent on silencing the hostile Stade Vélodrome crowd, with Malick Thiaw seeing a looping fourth-minute header cleared off the line by Pierre-Emile Hojbjerg.
Newcastle were ahead just two minutes later, and in-form Harvey Barnes was at it again. Sandro Tonali’s low cross from the right fell kindly for the winger, who fired home his fourth goal in three games.
Marseille pushed for an equaliser with Aubameyang at the heart of their efforts, but he was denied by Nick Pope after producing a sharp turn to work the space for a shot.
Igor Paixao curled just wide for the hosts, before Aubameyang missed two great opportunities late in an entertaining half. First, the striker headed wide from close range, before flashing his next chance wide as he tussled with Thiaw.
Newcastle were one of just four teams pre-round yet to concede a first-half UCL goal this term, and though they continued that record here, their clean sheet was wiped out just 19 seconds after half-time.
Pope raced out to meet a through ball, but Aubameyang got there first, before brilliantly curling inside the post from wide on the right. Within four minutes, the striker had completed the turnaround.
Timothy Weah crossed from the right, and Aubameyang stole in front of his marker to poke home. It was his eighth goal in 10 meetings, and his sixth goal contribution in five UCL games this term.
Newcastle were far from out of it, and Joe Willock forced Geronimo Rulli to tip over just before the hour mark.
The visitors were aiming to avoid a fourth successive away defeat across all competitions, and though Barnes curled wide of the far post four minutes from time, Aubameyang’s double proved decisive.
It earned Marseille only their second win in five UCL games this term, while Newcastle remain on nine points, but are still well placed to qualify for the knockout stages.
Flashscore Man of the Match: Pierre-Emerick Aubameyang (Marseille)