Both players were also absent for United's 1-0 Champions League defeat to FC Basel, with Jones out of action with a thigh injury and Bailly struggling with a problem he picked up on international duty.
Mourinho had previously suggested Bailly could come into contention for Saturday's game at Old Trafford but has now once again ruled both players out.
"They are out," he told MUTV when asked about Jones and Bailly. "But we are okay because we have Smalling, Rojo and Lindelof."
Mourinho also confirmed that Zlatan Ibrahimovic is again set to feature for the third game in a row: "I prefer him on the pitch than off the pitch.
"On the pitch he’s another option for us and he’s an option of quality. His physicality and his intelligence, the way he moves, the way he plays.
"But he needs time. We managed to give him 15/20 minutes in both matches, he needs more of that, so hopefully tomorrow we play him again."
Paul Pogba has impressed since his return from injury, playing a starring role in the win over Newcastle United in his first game back, and Mourinho has revealed he is still of the mind that he needs to protect the Frenchman.
He continued: "Paul is still on this process where he cannot reach the fatigue limit, he cannot go more than 65 to 70 minutes because that’s when fatigue normally arrives and with so many matches consecutively we need to protect such an important player for us."
United will be aiming to keep pace with City at the top of the Premier Leauge table, with Mourinho's men currently trailing Pep Guardiola's side by eight points after 12 matches.