The England international gave the Bavarians an early lead, scoring nine minutes into the Round of 16 first-leg clash at Allianz Arena.
Michael Olise delivered a precise cross into the box, allowing the former Tottenham Hotspur captain to head past goalkeeper Matej Kovar and end his four-match goal drought.
With that strike, he has now reached the 30-goal mark in a season for the seventh time in his club career, a feat he first achieved in the 2014-15 campaign.
Only Poland international and Barcelona striker Robert Lewandowski has recorded more 30+ goal seasons (nine) among players in Europe’s top five leagues.
In the 75th minute, he sealed his brace from the penalty spot, giving Vincent Kompany’s side a commanding three-goal advantage heading into the second leg at the BayArena on March 11.