Navas has been absent since early February with a hamstring injury, while a calf problem had kept striker Bony out of action since the beginning of January.
Both players have finally shaken off the injuries and will come back into the fold as the Citizens look to pick up the first trophy of the season this weekend.
There was also big news on Vincent Kompany, Bacary Sagna and Raheem Sterling, whose participation at Wembley was questioned after the trio trained away from their team-mates on Friday morning, but Pellegrini is optimistic that they will be fit following the Champions League win away to Dynamo Kiev on Wednesday.
“Sagna, Kompany and Sterling are recovering separately after the game but I hope the three of them will be fit," the Chilean told a press conference, via the club's official website.
“Mangala, Navas and Bony are training normally and are available for selection."
The Sky Blues can ill afford to lose Kompany, Sagna or Sterling, who were excellent in their midweek excursion to Ukraine.
Captain Kompany looked at the peak of his powers in the heart of City's defence, while Sterling picked up an assist for his side's second goal through David Silva.