Dortmund boss Thomas Tuchel said the 27-year-old was left out for "internal reasons".
Tuchel said "the matter is now settled" and Gabon forward Aubameyang will return to the side for Saturday's Bundesliga trip to Hamburg.
His replacement Adrian Ramos scored the only goal against Sporting.
Former Hertha Berlin striker Ramos rose to meet Matthias Ginter's cross and looped a header into the corner of the net.
Aubameyang, dressed in a black coat, scarf and fedora hat, watched the match from the stands.
Match ends, Borussia Dortmund 1, Sporting Lisbon 0.
Second Half ends, Borussia Dortmund 1, Sporting Lisbon 0.
Sebastian Rode (Borussia Dortmund) wins a free kick in the defensive half.
Foul by Sebastián Coates (Sporting Lisbon).
Offside, Sporting Lisbon. Adrien Silva tries a through ball, but Gelson Martins is caught offside.
Offside, Borussia Dortmund. Adrián Ramos tries a through ball, but Lukasz Piszczek is caught offside.
Delay over. They are ready to continue.
Delay in match Ezequiel Schelotto (Sporting Lisbon) because of an injury.
Julian Weigl (Borussia Dortmund) wins a free kick in the defensive half.
Foul by Adrien Silva (Sporting Lisbon).
Julian Weigl (Borussia Dortmund) wins a free kick in the defensive half.
Foul by Adrien Silva (Sporting Lisbon).
Foul by Raphael Guerreiro (Borussia Dortmund).
Gelson Martins (Sporting Lisbon) wins a free kick on the right wing.
Substitution, Sporting Lisbon. Lazar Markovic replaces Bryan Ruiz.
Attempt missed. Bryan Ruiz (Sporting Lisbon) header from the left side of the six yard box is just a bit too high. Assisted by Ezequiel Schelotto with a cross.
Attempt missed. Sokratis (Borussia Dortmund) header from the centre of the box is too high. Assisted by Marc Bartra with a headed pass following a corner.
Corner,  Borussia Dortmund. Conceded by Rui Patrício.
Attempt saved. André Schürrle (Borussia Dortmund) right footed shot from outside the box is saved in the bottom right corner.
Marvin Zeegelaar (Sporting Lisbon) is shown the yellow card for a bad foul.
Lukasz Piszczek (Borussia Dortmund) wins a free kick in the attacking half.
Foul by Marvin Zeegelaar (Sporting Lisbon).
Christian Pulisic (Borussia Dortmund) wins a free kick in the attacking half.
Foul by Rúben Semedo (Sporting Lisbon).
Attempt missed. Adrien Silva (Sporting Lisbon) right footed shot from outside the box is too high. Assisted by Bryan Ruiz.
Adrián Ramos (Borussia Dortmund) wins a free kick in the attacking half.
Foul by Sebastián Coates (Sporting Lisbon).
Substitution, Borussia Dortmund. Sebastian Rode replaces Mario Götze.
Substitution, Borussia Dortmund. Lukasz Piszczek replaces Gonzalo Castro.
Attempt missed. Adrien Silva (Sporting Lisbon) right footed shot from outside the box is just a bit too high from a direct free kick.
Raphael Guerreiro (Borussia Dortmund) is shown the yellow card for a bad foul.
Foul by Raphael Guerreiro (Borussia Dortmund).
Adrien Silva (Sporting Lisbon) wins a free kick in the attacking half.
Foul by Raphael Guerreiro (Borussia Dortmund).
Gelson Martins (Sporting Lisbon) wins a free kick in the attacking half.
Attempt saved. Raphael Guerreiro (Borussia Dortmund) left footed shot from outside the box is saved in the bottom left corner.
Adrián Ramos (Borussia Dortmund) wins a free kick in the attacking half.
Foul by Sebastián Coates (Sporting Lisbon).
Gonzalo Castro (Borussia Dortmund) wins a free kick in the defensive half.
Foul by Adrien Silva (Sporting Lisbon).
Striker Pierre-Emerick Aubameyang was dropped by Borussia Dortmund, who beat Sporting Lisbon to reach the last 16 of the Champions League.