The arrival of Ivory Coast international Bony from Swansea in January meant City had one more foreign player in their squad than they are permitted to register for European competition.
Governing body UEFA published City's revised squad for the second half of the season on Thursday and Jovetic's name was not included.
The decision by manager Manuel Pellegrini to leave out Jovetic means that he will continue to be restricted to just three senior strikers for the remainder of the competition - now Bony, Sergio Aguero and Dzeko.
But given 25-year-old Jovetic's limited involvement during 19 often injury-troubled months at City, Pellegrini - despite a looming Champions League last-16 tie against Barcelona - has maybe decided it is a sacrifice worth making.
Jovetic, who missed large spells last season with calf and hamstring problems, has scored just 11 goals since his £22million move from Fiorentina in 2013 and this latest setback will raise doubts over his long-term City future.
The issue has arisen because City, as punishment for breaching UEFA's Financial Fair Play restrictions, are restricted to naming just 16 foreign players in their squad rather than the usual 17.
City had to submit their squad by 11pm on Tuesday, but the details have only now been made public by UEFA.
The other prime candidates for omission were thought to be back-up goalkeeper Willy Caballero and full-backs Aleksandar Kolarov and Bacary Sagna
Frenchman Gael Clichy and Belgian Dedryck Boyata do not count on the foreign quota as they qualify as homegrown and club-trained respectively.
By leaving out Jovetic, the balance of the squad is not changed
Pellegrini's initial decision to name just three strikers was influenced by injury to Alvaro Negredo, who has subsequently joined Valencia on loan, last summer
City host Barca in the first leg of their first knockout round tie on February 24 and travel to the Nou Camp three weeks later.
Source : PA
Source: PA