The Cote d’Ivoire international has been on the sidelines since November 18 after going under the knife to fix a knee injury.
Following his lengthy absence in Jose Mourinho's squad, Bailly made his comeback as a substitute for Lukaku in the 93rd minute on Saturday for his first competitive game since Manchester United’s 1-0 defeat to Chelsea on November 5.
And the former Villarreal defender expressed joy as Lukaku’s brace guided the Old Trafford outfit past David Wagner's side at the John Smith's Stadium.
“Happy for having qualified for the quarterfinals and happy to be back,” Bailly wrote on Instagram.
Manchester United welcome Brighton and Hove Albion to Old Trafford for their FA Cup quarter-final tie on March 16.