Thiago hit back in the first half after les Gones raced into a two-goal lead but the Ligue 1 side held out to reach the Coupe de la Ligue showpiece against the French championsAlexandre Lacazette and Bafetimbi Gomis sealed a 2-1 win for Olympique Lyonnais in Wednesday's Coupe de la Ligue semi-final with Troyes.
Les Gones's No.10 swept home after 16 minutes and his attacking partner doubled the advantage following a clever team move, but Thiago stabbed home from a corner to give the Ligue 2 side hope.
However, there was to be no further giant-killing for the visitors, as Lyon booked their place in the final to face Paris Saint-Germain where they will search for their second Coupe de la Ligue triumph after winning the trophy in 2001.
Lyon controlled the tempo in the early stages and were rewarded with the opening goal after 16 minutes.
Right-back Zeffane received the ball on the overlap and had time to pick out Lacazette, who duly side-footed home from 12 yards.
Briand was a constant menace for Lyon on the left and he was influential in the second goal on 27 minutes.
The winger received Lacazette's neat throughball in the box and crossed to the near post, where Gomis applied the finishing touch from inside the six-yard box.
Soon afterwards, Gomis flashed an effort across goal from a tight angle as Lyon piled on the pressure.
Home goalkeeper Anthony Lopes had to be alert at the other end, however, producing a fine fingertip save from Benjamin Nivet's volley.
But there was nothing he could do to prevent Thiago halving the deficit after 35 minutes.
The Lyon defence failed to deal with a corner from the left and the Brazilian was on hand to smash the ball home from close range.
The match followed a similar pattern after the break with Lyon largely dictating play, while Troyes continued to threaten at set-pieces.
Lyon had the ball in the net for a third time on the hour mark when Briand guided a header over Matthieu Dreyer, but the celebrations were cut short by the offside flag.
Kone also thought he had increased the advantage with 15 minutes remaining when he flicked home Gomis' header, but he too was ruled offside.
Lacazette then forced a smart stop from Dreyer in the closing stages, as Lyon saw out the remaining minutes despite a spirited late effort from the visitors.