كتب : Hatem Maher
The Nigerian striker, who made his competitive debut in Ismaili's 2-1 African Champions League defeat by bitter rivals Ahli last month, netted the winner on 71 minutes after a solo effort.
The victory hands Ismaili a timely boost after they made a dreadful start to their season as they lost their first two matches in the Champions League group stage.
It was also the first win for Dutch coach Mark Wotte, who took over at the club in the summer following the resignation of Emad Soliman.
Ismaili, who still suffer from the creativity problem that costs them dearly, looked out of sorts in the first half.
Petrojet had the upper hand despite selling two key players, playmaker Walid Soliman and holding midfielder Mohamed Shaaban, in the close season.
Their striker Sayed Hamdi failed to head home from close range after being picked out unmarked by a neat cross in the 30th minute.
Midfielder Kamal Ali was also unlucky not to break the deadlock seven minutes before the break when his curling shot from inside the area went just wide of the post.
Petrojet also struck the bar early in the second half via a powerful volley from Tamer Moheb.
Ismaili then took control and squandered two clear-cut chances to grab the lead.
Off-form striker Ahmed Ali could not apply the finishing touch after breaking clear of defense while skipper Mohamed Hommos hit the side netting with the goal at his mercy.
Godwin, who joined Ismaili after ending a short spell with Libyan side Nasr, made amends in the 71st minute to give his new side a precious win.
He gathered a pass from substitute Mohsen Abou-Greisha and skipped past his challenger on the edge of the area before sending a low shot past the advancing keeper and into the net.