The 27-year-old opened the scoring for the Horses in the 45th minute after firing past goalkeeper Zvonimir Mikulic inside the penalty area.
Michel doubled the lead in the 86th minute while the hosts put one back courtesy Ziguy Badibanga’s penalty in the closing stages of the game.
Qarabag were underdogs going into the game having been held to a 0-0 draw at home. But with this victory, they have booked a place to the play-off round.
The goal is Ndlovu's third goal in the competition this season for the Azerbaijan topflight outfit.