The surprise win was Hertha's first over the Bavarian giants in nine years and came courtesy of first-half goals to Vedad Ibisevic and Ondrej Duda.
Leckie came on with 20 minutes remaining in the match, replacing captain and ex-Chelsea star Salomon Kalou on the right wing.
The 27-year-old had limited chances up front but repaid the faith with a solid defensive effort against both Franck Ribery and David Alaba.
Bayern's shock loss is their first of the season under Niko Kovac and leaves them level on points with Leckie's Hertha through the first six games of the season.
Socceroos captain Mile Jedinak had a more difficult time of things with Aston Villa, settling for a 1-1 draw away to a Bailey Wright-less Bristol City in the Championship.
The 34-year-old played 90 minutes in the heart of the defence alongside James Chester as Birkir Bjarnason cancelled out Josh Brownhill's early effort for the home side.
After sitting out Villa's opening league match of the season, Jedinak has since become a regular fixture in Steve Bruce's line-up and will look to cement his status as the Birmingham-based club chase Premier League promotion.
In the Czech First League, Golgol Mebrahtu came off the bench in Sparta Prague’s 1-0 loss to Viktoria Plzen.
With Sparta trailing courtesy of an Uros Radakovic own goal, Mehbrahtu’s introduction appeared to spark some life into the away side.
That was until a horrendous Nicolae Stanciu challenge reduced Sparta to 10 men late in the contest, all but ending their hopes of an equaliser.
The loss, Sparta’s first of the season, sees them surrender second place in the process with two thirds of the season still left to play.
Meanwhile, Sebastian Pasquali played 77 minutes in Jong Ajax’s 3-0 defeat to FC Eindhoven in the Eerste Divisie.
The talented 18-year-old was substituted after goals from Alvin Daniels and Collin Seedorf, nephew of Netherlands legend Clarence, sent the away side on their way.
The loss leaves Pasquali and co. in 10th position through seven games, a far cry from their league title triumph last season.
And Ange Postecoglou's Yokohama F. Marinos continue their late-season push for J1 League survival when Vegalta Sendai visit the NHK Spring Mitsuzawa Football Stadium later on Saturday afternoon.
Postecoglou's men sit just two points above the relegation zone with seven matches remaining in the season.
