They lost by 26 runs against The Unlimited Titans in a domestic T20-match at SuperSport Park on Sunday.
Parnell, an international left-arm swing bowler who has shown glimpses of the form which made him a match-winner for the Proteas, hurt his finger on Friday evening.
He did not pass a fitness test for the Ram Slam T20 Challenge match against The Unlimited Titans.
Paul Adams, the Cape Cobras coach, said the bowling attack possibly conceded 20 runs too many on Sunday, partially because of ill-discipline.
The pitch assisted the spinners as it offered turn to the slower men, and that contributed to the slightly sedate finish of the Cape Cobras, who made 147 for six.
The two teams were virtually in the same position after 11 overs, but the Titans flourished thanks to the belligerent Farhaan Behardien, who hammered 61 off 31 balls.
The chase of the Cobras, who had to purse the target in conditions that benefited the spinners later on in the game, petered out a tad and they finished on 147 for six.
Adams acknowledged that the Cape champions are missing the experience of hard-hitting and well-travelled campaigners like Dane Vilas and Kieron Pollard.
Vilas is the South African wicketkeeper currently on duty in India.
Pollard is representing the West Indies against Sri Lanka in a T20-series and will only be available for the Ram Slam match against the Sunfoil Dolphins on Sunday at SuperSport Park in Centurion.
The current players who are operating in the middle-order like SA Engelbrecht and Lesiba Ngoepe are not extremely experienced at Ram Slam T20 Challenge-level and are still developing their trade in the shortened format.
The Cape Cobras have suffered misfortune due to injuries to Rory Kleinveldt (shoulder), Robin Peterson (finger), Tshepo Moreki (foot), Andrew Puttick (mouth infection) and Parnell (finger).
Adams said they are hopeful Parnell will recover in time for the Ram Slam T20 Challenge clash against the VKB Knights in Kimberley on Wednesday.