The Chilean boss controversially dropped Stevan Jovetic from his European squad in order to include new signing Bony for the remainder of the competition.
The Citizens were handed a continental squad cap towards the end of last season for failing to comply with Financial Fair Play regulations and, as a result, are restricted to naming just 16 foreign players.
The expected introduction of Ivory Coast striker Bony meant that one unlucky player was to miss out – Pellegrini choosing Jovetic ahead of fellow nominees Bacary Sagna and Willy Caballero.
For a player of Jovetic’s calibre, it’s an incredibly harsh decision but City’s manager has revealed to the press that Bony’s unique qualities inside the area were ultimately the deciding factor.
“It is always difficult to take a player out of the list but we have restrictions this year,” Pellegrini explained to reporters.
“We brought Bony because I think that we need another striker, a box player, and in the position of Jovetic maybe we have some other options. It is a difficult decision but I think it was the best for the squad.”
The Etihad outfit were once again handed a tough Champions League draw in the last-16 as they were paired with La Liga giants Barcelona in a repeat of last season’s knockout stage encounter.
The Catalans triumphed comfortably enough on that occasion, but with the added physical presence and aerial threat from Bony, City may feel that they stand a better chance this time around.