Jose Mourinho's team enjoyed a good group campaign, recording five wins from their six group games.
Basel won 2-0 at Benfica to qualify second.
United are leading Group A with 12-points, and they are all but guaranteed a spot in the last 16. The Italian champions go through behind Barcelona, who rounded off their group phase by easing to a 2-0 win at home against Sporting Lisbon.Lionel Messi was left on the bench at a sparsely populated Camp Nou as Paco Alcacer headed the hosts in front and Jeremy Mathieu then scored an own goal against his old side.
Just a reminder that you can not play opponents from the same country in the last 16 or teams you have played in the group stages.
Paul Pogba highlighted once more why he is a footballing genius after another solid show which helped Manchester United beat CSKA Moscow at Old Trafford in a pivotal Champions League Group A encounter.
The contrast in quality of teams that Manchester United could face in the Round of 16 stage is vast.
Chelsea drew 1-1 with Spanish side Atletico Madrid at Stamford Bridge. Chelsea looked brilliant over the weekend, beating Newcastle 3-1, led by 2-goals from Eden Hazard.
Elsewhere, Roma recorded a 1-0 win over Qarabag at the Stadio Olimpico.
The Swiss outfit got off to the perfect start when Mohamed Elyounoussi headed them into a fifth-minute lead from Michael Lang's cross. Juventus also beat Olympiakos 2-0 to secure second spot to continue to round 16.
Champions League action will continue Wednesday evening when the teams' fates in the last four groups will be decided.
Liverpool won their group after hammering Spartak Moscow 7-0 at Anfield tonight.
In Group H, Tottenham have already finished top, with Real Madrid second place three points behind.
CSKA struck out of the blue as Mario Fernandes broke down the right and set up Vitinho, whose miscued shot struck Dzagoev in the back and bounced into the net.