The talented winger was introduced at halftime instead of the ineffective Sherif Ashraf.
He made up for Gamal Hamza's wasted penalty when he scored two minutes past the hour mark with a delightful curling effort.
The Cairo giants' first victory in three matches moved them to fourth place in the league table with 30 points, one behind third-placed Al-Gaish, who still have a game in hand.
Zamalek failed to put in a convincing display as their uninspiring form prompted their fans to chant angry slogans against coach Ruud Krol.
The club's board is set to decide on Sunday whether to sack the Dutchman, with several Egyptian names being linked with Zamalek's managerial job.
Baladeya could have been in front in the 18th minute when they were awarded a deserved penalty.
Gamal Gad got the better of Beshir Al-Tabie inside the area, leaving the combative defender with no alternative but to bring him down.
Gad stepped up but his effort was blocked by Zamalek keeper Mohamed Abdul-Monsef.
Shikabala's second-half introduction revived Zamalek's attacking options.
The former PAOK wizard provided pinpoint passes to his teammates, who failed to capitalize on numerous goalscoring opportunities.
Shikabala's superb chip picked out Hamza inside the area on the hour mark. The forward was tripped by Baladeya keeper Atef Al-Saied as the referee pointed to the spot.
Al-Saied made amends for his mistake when he blocked Hamza's spot-kick.
Shikabala scored the winner in the 62nd minute when he controlled a pull-back on the edge of the area, spun around before hitting a superb left-footed curling effort into the top corner.