Aliadiere volleyed home three minutes into added time as Lorient joined Troyes, who beat Nancy 3-0 at home earlier on Tuesday, into the last four.
"It's a nice goal but the most important thing is that it sends us to the semi-finals," Aliadiere told Eurosport.
Saint-Etienne, who will play the League Cup final against Stade Rennes on Saturday, got off to a good start but Brandao squandered two chances at the half hour.
Les Verts were caught cold one minute before half-time when Maxime Barthelme fired a shot from just inside the box into the top corner to put the visitors ahead.
Lorient came close to doubling the advantage in the 67th minute but Stephane Ruffier pulled a brilliant save to deny Aliadiere from point-blank range after the former Arsenal forward had been set up by Benjamin Corgnet.
Pierre-Emerick Aubameyang, who came on as a second-half substitute, latched onto a Renaud Cohade cross from the right to equalise in the 74th minute.
However, at the end of a sharp counter-attack, Aliadiere volleyed a perfect Mathias Autret cross under the bar that silenced the home crowd.
"The idea was to defend well and hit them on the break," said Aliadiere.
It was Saint-Etienne's first defeat in all competitions since a 1-0 loss at Olympique Marseille in Ligue 1 on December 23.
At Troyes's Stade de l'Aube, defender Jeremie Brechet headed home from a corner to put the hosts ahead seven minutes into the second half.
Winger Julien Faussurier doubled the tally in the 75th minute, firing past Damien Gregorini after being set up by Fabien Camus.
Camus then collected Faussurier's cross to put the result beyond doubt from close range 10 minutes from time.
On Wednesday, second division RC Lens entertain Girondons Bordeaux before Paris Saint-Germain face Evian Thonon Gaillard away.
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