Liverpool face Lyon, Fiorentina and Debrecen while Chelsea play Porto, Atletico Madrid and APOEL Nicosia.
The England center-back is likely to miss Wednesday's Champions League tie with Apoel Nicosia, but should be fit to face Everon next weekend.
And Apoel took early advantage as Marcin Zewlakow stole in to strike after only six minutes as Chelsea appealed in vain for offside.
It was just reward for Apoel's fans, who provided magnificent and noisy backing for their side throughout on a rain-soaked night at Stamford Bridge.
In the Champions league Champions League Barcelona, Real Madrid, Bayern Munich, and Chelsea all move on at the expense of Milan, APOEL, Marseille and Benfica.
Mourinho, whose Real team are set to succeed Barcelona as La Liga champions, was full of praise for Cypriot minnows Apoel Nicosia after their quarterfinal tie.
The Romanian side, along with Wolfsburg, Rubin Kazan, AZ Alkmaar, Standard Liege, Debrecen, APOEL Nicosia and FC Zurich, make their Champions League debut in this year's tournament.
APOEL, who have played just 49 Champions League matches compared to Real's record total of 343, have already upset the odds to make it this far in the competition.
Chelsea, the 2007 finalists and bidding for a first title under Carlo Ancelotti, are seeded in Group D where they meet two-time champions Porto, Atletico Madrid and Cypriots APOEL Nicosia.
"I think in a few years people in Cyprus will realize what Apoel have done, it is the biggest achievement in Champions League this season, " Mourinho said after his side's 8-2 aggregate victory.
APOEL's unlikely run continued in the round of 16 with a dramatic penalty shootout victory over former French champions Lyon -- who had reached the knockout stages in each of the previous eight seasons.
Esteban Solari hopes his brother would not begrudge APOEL a semifinal berth, where the minnows would face either 1993 winners Marseille of France or Germany's four-time European champions and 2012 final hosts Bayern Munich .
The Blues were unperturbed by this early setback and Essien restored equality after 19 minutes when he took a pass from Florent Malouda and fired a swerving shot past Apoel keeper Dionisios Chiotis, who had no chance.
And with one game for the Blues remaining in the group stages - at home to Apoel Nicosia on 8 December - Atletico Madrid remain the only club to have scored against them in this year's competition.
Didier Drogba's excellent finish from Yuri Zhirkov's cross put Chelsea ahead and they seemed on course to end the first phase of their assault on the Champions League with a victory until Apoel substitute Nenad Mirosavljevic raced clear to equalise with three minutes left.
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