The Belgian came off late in Wednesday night's 2-1 EFL Cup win over Swansea City after getting through most of his return to action, having not featured since May after succumbing to a soft tissue injury in the Champions League against Real Madrid.
It is understood that Kompany could be sidelined for several weeks with a hamstring injury which could prompt Guardiola to become active in the transfer market in January.
City showed interest in Bonucci during the summer but Juventus' asking price of £50million and the fact Kompany was progressing well from the thigh problem he sustained late last season had cast plenty of doubt over a potential deal.
Guardiola allowed Eliaquim Mangala and Jason Denayer to join Valencia and Sunderland respectively and further injury worries relating to Kompany may force another chase for Bonucci as City have just John Stones and Nicolas Otamendi fit while Aleksandar Kolarov as a makeshift centre-back option.
The Spanish tactician previously referred to the 29-year-old Italy international as one of his favourite players and now has to decide whether or not to plot another swoop for his services as the winter window approaches.