His first came in the 51st minute as he tapped home a Robert Lewandowski cross to give the visitors the lead at Stamford Bridge.
Gnabry added another just three minutes later, tapping home yet another pass from the Polish star.
Lewandowski added a goal of his own later in the second half after Alphonso Davies' dazzling run down the left ended with him laying the ball into the No.9's path.
And, following Bayern's triumph on Tuesday, Gnabry took to Twitter to declare that "London's still red!" in celebration of the victory.
— Serge Gnabry (@SergeGnabry) February 25, 2020
Tuesday's two-goal performance was not Gnabry's first starring performance in London this season, as the winger previously netted four goals against Tottenham in the group stage.
The 24-year-old has scored more goals in London than any player in the Champions League this season , with the Bayern star's six being one more than five scored by Harry Kane in Tottenham's home matches.
Gnabry originally played in London from 2011-16 having joined Arsenal's academy from Stuttgart at the age of 16.
His senior debut with the Gunners came in October 2012 as he became Arsenal's second-youngest player in Premier League history behind only midfielder Jack Wilshere.
Gnabry went on to make 18 total appearances during his time at the Emirates Stadium, scoring one goal, before making a move to West Brom on loan.
His time with the Baggies produced only three appearances, as Gnabry went on to find success in Germany shortly after.
Gnabry now has 17 total goals for Bayern this campaign as the defending champions sit top of the Bundesliga table.
Bayern are set to face Hoffenheim this weekend before taking on Schalke in the DFB-Poka quarter-finals in midweek..