Koke got Atletico's first at the Wanda Metropolitano after two minutes and France international Antoine Griezmann scored the second mid way through the first-half.
Not even the dismissal of Stefan Savic for his second bookable offence eight minutes from time could spark Monaco.
Radamel Falco missed a penalty and the French side, runners-up to Paris Saint-Germain last season, are not in contention for a place in the Europa League.
Borussia Dortmund sealed their spot along with Atletico from Group A following a 0-0 draw with FC Bruges.
In Group B, Christian Eriksen’s late goal at Wembley gave Tottenham Hotspur the points against Iner Milan.
The win moves Spurs into second place behind already qualified Barcelona while Inter drop to third. However on the last day of action in the group on 11 December, Inter have the easier task.
The Italians host bottom of the pool PSV Eindhoven while Spurs travel to Barcelona.
Porto beat Schalke 3-1 to confirm their position as winners of Group D. Schalke will go into the hat as runners-up.
Those two slots from from Group C will be decided in the final round of games. Napoli, Paris Saint-Germain and Liverpool all have a chance to advance.
Liverpool host Napoli on 11 December knowing that either a 1-0 win or a victory by more than two goals will allow them to continue.
PSG will progress with at least a draw at Red Star Belgrade irrespective of the result at Anfield.
“Sometimes when the draw is made for a competiton like this, the first two from the group are absolutely clear,” said Liverpool manager Jurgen Klopp. “But from the very first it has never been like that is in this group.”