Manchester United overcame an injury to Henrikh Mhkitaryan and a red card to Eric Bailly to qualify for the Europa League round of 16.
Coming into the second leg with a 3 - 0 first leg advantage, Jose Mourinho could have rested his star players for the match in France but named a strong starting eleven.
The likes of Mhkitaryan, Zlatan Ibrahimovic, Paul Pogba and Juan Mata all started the match which United won 1 - 0 courtesy of a first half Mhkitaryan goal.
The Armenian scored the only goal of the game when he converted Juan Mata's cross from the left with the faintest of touches.
His night was cut shot however due to an injury which forced him off the pitch and replaced by Marcus Rashford.
The match was evenly balanced and the French side could have equalized but for smart goalkeeping by Romero who saved Perrin's header.
In the 63rd minute Eric Bailly was shown a second yellow card for a rough tackle.United held on for the lead however.
The win sees Saint-Etienne defeated 4-0 on aggregate as United progress to the UEFA Europa League last-16.
Meanwhile other teams to play on Wednesday and qualify for the Europa League last-16 draw which will be held on Friday are Krasnodar and FC Schalke 04.