The hosts led 2-1 at the break thanks to efforts from Henri Saivet and Cheick Diabate, with Sadio Diallo's equaliser sandwiched between them.
However, Hoarau registered his first goal since returning to France from Chinese side Dalian Aerbin in January to hand Bordeaux a two-goal cushion 18 minutes from time.
Lamine Kone's scrappy effort after 84 minutes proved to be simply a consolation as Bordeaux extended their unbeaten run against Lorient to six matches.
Saivet, scorer of the winner in Saturday's 2-1 triumph over Evian, headed home after 22 minutes, only for Diallo to evade a number of Bordeaux challenges to level four minutes later.
Diabate's left-footed finish ensured that the hosts went in ahead at the break with Hoarau scoring his first goal in France since netting in a UEFA Champions League win over Dinamo Zagreb in November 2012.
Despite Kone registering his opening goal of the campaign, Bordeaux held out for the win as Gillot's side moved seventh in Ligue 1 - five points behind Saint-Etienne in the UEFA Europa League qualification spot.
Lorient have now lost their last three league games and have won just one of their last eight top-flight matches.