The Italian was relieved of his duties ahead of the encounter but City was able to pull out the victory and clinch second place in the process.
Goals from Sergio Aguero and Edin Dzeko ensured the visitors secured an automatic place in the Champions League next season.
City showed it meant business in the early going when Aguero pounced on a loose ball and unleashed a shot that Alex McCarthy did well to save.
McCarthy then made a fantastic double stop moments later when he kept out James Milner’s effort before blocking the follow-up.
Reading had its goalkeeper to thank for the 0-0 scoreline approaching the half-time interval but the youngster was finally beaten when David Silva set up Aguero on a platter to open the scoring.
It was a deserved lead for the visitors who were undoubtedly thankful that they had something to show for their dominance in the first 45 minutes.
Reading almost equalized five minutes after the restart when Pavel Pogrebnyak outmuscled two defenders to direct a header at goal that Joe Hart tipped away.
Yaya Toure then tried to double City’s advantage, but once again McCarthy was up for the task and Reading remained in the game.
The home side turned on the pressure with 15 minutes to go and was almost rewarded but Carlos Tevez headed Nick Blackman’s effort off the line.
It was a close call for Manchester City who were on the back foot a little bit until substitute Edin Dzeko put the game to bed with two minutes remaining.
David Silva was once again the architect as he found Dzeko in the penalty area, and the Bosnian cut inside before unleashing a shot that beat McCarthy.
Manchester City are now guaranteed an automatic place in the Champions League following the win and started the post Mancini era with a victory.