The Ivorian centre-back has had a number of injury problems this season and has only managed 16 appearances in all competitions for the Red Devils.
However, according to Manchester Evening News, it was a bout of sickness which kept Bailly out of the defeat of Spurs.
Bailly was not named in Uniteds squad which beat West Brom and was an unused substitute in the sides defeat of Bournemouth.
Its claimed the defender had been vomiting before the West Brom match and Mourinho decided to leave him out of the clash with Tottenham as a precaution.
United are confident that Bailly will be available for the sides clash with Arsenal at Old Trafford at the weekend.
Chris Smalling and Phil Jones, though, will hope to continue in central defence after impressing at Wembley.