كتب : Hatem Maher
The 24-year-old opened the scoring after 18 minutes but Petrojet's top scorer Eric Bekoe cancelled out his effort after converting a penalty four minutes later.
Shikabala restored Zamalek's advantage five minutes past the hour mark before Gaafar rounded off a neatly-worked counter attack seven minutes from time to make sure of the victory.
He took his tally to seven goals in as many games.
Bekoe scored from the spot again deep into stoppage time to notch a consolation and regain his position on top of the scorers' chart with 13 goals, one ahead of Nigerian Minusu Buba of Police Union.
Zamalek's seventh successive win under coach Hossam Hassan lifts them to third spot in the table with 35 points, seven behind leaders and arch-rivals Ahli.
The Cairo side, who faced the unthinkable prospect of being relegated to the second division prior to the arrival of Hassan, revived their hopes of launching a late assault on the title.
They won the last of their 11-league titles in 2004 under Portuguese tactician Nelo Vingada.
Petrojet remain second on 35 points but they wasted the chance to close to within two points of Ahli.
Balanced Half
Hussein Yasser, who joined Zamalek as a free agent in January, made his first start after putting in some fine displays off the bench in the past few games.
He played alongside Shikabala to support lone striker Gaafar, the only reliable frontman at Hassan's disposal.
Petrojet welcomed back Ghanaian striker Bekoe, who served a two-game suspension.
The first-half was an evenly-balanced contest, with both sides struggling to break down opposing defense.
Zamalek took the lead though after 18 minutes through a superb free-kick maneuver.
A touched-on free kick went to Shikabala, who released Sabri Rahil down the left with a deft first-time pass.
Rahil, who deputized for the suspended Mohamed Abdul-Shafi, pulled the ball back to Gaafar to send a half volley past Petrojet keeper Ahmed Fawzi.
Petrojet equalized few minutes later when Bekoe sent keeper Abdul-Wahed Al-Sayed the wrong way from the spot after central defender Amr Al-Safti needlessly fouled Petrojet playmaker Walid Soliman.
Upper Hand
Zamalek gained the upper hand after the break to outplay Petrojet, thanks to some neat combination between Gaafar, Yasser and Shikabala.
Shikabala, who was unlucky not to score earlier in the game, put Zamalek in front again with a fine low shot from the edge of the area after a clever dummy from Gaafar.
A swift breakaway in the 83rd minute helped Zamalek add the third to kill off the hosts' hopes.
Shikabala lofted the ball over a challenger to find pacey right-back Ahmed Ghanem, who ran down the right flank, skipped past Osama Mohamed and reached the byline.
Ghanem waited until Fawzi rushed out of his goal before sending a low cross to Gaafar for an easy tap in.
Petrojet were awarded another penalty just before the final whistle when substitute Ahmed Magdi handled a cross inside the area.
Bekoe converted the ensuing penalty but Zamalek held on for a precious win.