It always appeared a case of when rather than if United would progress to the last 16 for the first time since 2013 14, despite their winning start to Group A ending with the last-gasp defeat at Basel.
Not even Alan Dzagoev’s controversial opener had the Old Trafford faithful concerned as only a record seven-goal defeat would deny United, who turned things around through quick-fire Romelu Lukaku and Marcus Rashford goals to triumph 2-1.
“We confirmed out progression but in the way we wanted to,” said Mourinho. “We played well and got the result. At half-time we were playing well and I was not unhappy. The boys played professionally.
“If I could choose goal-scorers, I would always choose the strikers. Their confidence depends on that sometimes. Romelu Lukaku’s work for the team every match is crazy. The goal was important for Marcus Rashford too.
“Luke Shaw offensively was very good and made a great contribution for the team. Sergio Romero is only on the bench this season because we have David de Gea.
“The first impression for the first goal was offside but then we saw it was not. The team showed the desire in the second half not by losing and going through, but to win.
“Shaw had waited for a long time, it is not easy to give an opportunity to a player in matches when we need results. I wanted to make changes, but Luke managed 90 minutes and I told him it is a opportunity to increase his levels.”
Victory puts United among the group winners for the last-16 draw and saw them equal the club record of 40 successive home games without defeat ahead of Sunday’s visit of runaway Premier League leaders Manchester City.
Mourinho’s men dominated from the outset and were aggrieved to be behind at half-time, with many players claiming offside against Dzagoev as Vitinho’s shot went home off his back.
It mattered little as Lukaku stayed strong to direct home a fine Paul Pogba pass, with Rashford keeping his cool to wrap up victory.
Buoyed by impressive back-to-back away wins at Watford and Arsenal, Mourinho made six changes with half an eye on this weekend’s crunch clash with City.
A subdued pre-match atmosphere was compounded by the accidental omission of the Champions League theme tune, but a bright start soon saw volume inside Old Trafford rise.
Smart build-up play by Lukaku saw Rashford put behind the CSKA backline, with the forward’s shot bobbling across goal and off the far post inside four minutes.
They continued to push and Juan Mata’s exquisite control from a long ball brought the next clear-cut chance, Rashford denied by Igor Akinfeev.
The hosts were looking dangerous down the flanks and Luke Shaw was impressing on his first start in 219 days, with the left-back seeing an acrobatic attempt from an acute angle denied.
The 22-year-old was showing only the odd sign of rust and looked sharp on the attack, latching onto a Pogba pass only to hit a cross just out of Rashford’s reach.
Antonio Valencia saw half-hearted penalty appeals ignored as the first half petered out, only for CSKA to go ahead in controversial circumstances.
The Russians had failed to create a clear-cut opening but went in ahead after Mario Fernandes capitalised on a sloppy defensive line and burst down the right to send in a cross for Vitinho to strike home off Dzagoev’s back.
United players were angered that offside was not called against Dzagoev, but officials appeared to point to off-the-field Daley Blind playing him onside.
Rashford stung the palms when play resumed after half-time.
Chris Smalling nodded wide from Mata’s volleyed cross and Rashford’s free-kick took a slight deflection wide as United pushed for a deserved leveller that arrived in the 64th minute.
Pogba sent a superb wedged ball over the top to Lukaku, who showed impressive strength to hold of Viktor Vasin and direct past Akinfeev.
Just 66 seconds later United were ahead. Rashford raced onto fire in a looped Mata pass, showing impressive skill and no little composure.
Pogba curled over as the wind appeared to be taken out of CSKA’s sails, although Sergio Romero had to be alert to deny Dzagoev on a rare voyage forwards late on.
Romero, Lindelof, Smalling, Blind, Valencia (Tuanzebe 72), Shaw,Pogba, Ander Herrera (McTominay 67), Mata, Lukaku (Martial 74), Rashford.
Akinfeev, Vasili Berezutski, Vasin, Ignashevich, Fernandes, Golovin, Kuchaev, Nababkin (Khosonov 90), Vitinho (Zhamaletdinov 83), Chalov (Gordyushenko 68), Dzagoev.