Portuguese midfielder Joao Moutinho added to Mbappe’s goal with a superb curling strike to seal the victory and help move Monaco five points clear at the top of the French league.
However, Monaco’s triumph was marred by an injury scare to star striker Radamel Falcao who went off with a rib knock late on after a challenge from Bordeaux defender Nicolas Pallois.
That left the Colombian facing a race against time in order to be fit for Wednesday’s eagerly-awaited clash with City holding a 5-3 advantage from the first leg.
Falcao, who struggled to impress during spells in England with Manchester United and Chelsea, has rediscovered his eye for goal this term, having scored 22 goals in all competitions already.
WAITING GAME: Monaco are sweating on the fitness of Radamel Falcao
And Monaco manager Leonardo Jardim says he is hopeful the Colombian will be fit to face City.
“He took a heavy knock to the right of his hip,” the Monaco manager said. “We’ll take a look at what’s going on with it.
“I hope the injury is not a serious one, because if he is fit, he will start against Manchester City.”
Monaco had initially struggled to break down a well-organised Bordeaux.
But after good work from Falcao, 18-year-old Mbappe showed just why he has been compared to Thierry Henry by Arsenal manager Arsene Wenger by drilling home a crisp low shot in the 68th minute.
LETHAL WEAPON: Kylian Mbappe struck again for Monaco on Saturday
It was Mbappe’s 16th goal of the season, and 10th in the league.
Six minutes later, Moutinho doubled Monaco’s lead when he latched onto Bernardo Silva’s pass and curled in a stunning shot.
It was only Moutinho’s eighth goal in 117 league games since the Portuguese midfielder joined Monaco from Porto four years ago.
Not that Monaco are struggling in front of goal. Their overall tally is now up to 123 heading into the showdown with City.Monaco were given a late scare when Bordeaux striker Diego Rolan narrowed the deficit on 83 minutes to set up a nervy finale.
However, Monaco held on to put them in good heart ahead of Wednesday’s clash.