However, with Bailly now at the Africa Cup of Nations with the Ivory Coast and a full schedule of fixtures, Mourinho was forced to rotate the squad.
Speaking prior to the game, Mourinho wanted to give the pair a rest while he still had the players available to cover their positions.
“Against Middlesbrough, Bailly and Smalling started and I rested Jones and Rojo to have them fresh for the game,” Mourinho told Sky Sports.
“It was the last game Bailly plays as he is off to the Africa Cup of Nations.
“Then you see how some things are going as some players react different to others with the accumulation of matches.
“But again there are no excuses, It’s difficult for us, It’s difficult for West Ham. We are in the same situation so at the end of the match I hope the best team wins.”
They had been in brilliant form under Mourinho, playing a vital role in our unbeaten run, which was surprising as they had both failed to establish themselves in the first-team before that.
Hopes are they can maintain their impressive form moving foward as they claim another clean sheet, with Chris Smalling coming on in the second-half to help close out the game.