Wydad had started their campaign with defeat away to Algeria’s JS Kabilye, but skipper Yahya Jabrane’s 34th minute penalty was the difference at the Mohamed V Stadium in Casablanca.
The result sends them to third in Group A with three points while hitherto unbeaten Petro remain second on four points from a win and a draw.
Jabrane scored with a well taken penalty drilled straight through the middle after Pedro Francisco brought down Mohamed Ounajem inside the area.
Before that, both sides had chances, with Tiago Azulao twice coming close for Petr with shots which drilled wide.
For Wydad, Attiyat Allah came close with a shot dragged wide from the edge of the area.
In the second half, Petro piled down pressure on Wydad, especially trying to use set pieces but the home side held on to defend well.
Skipper Azulao had a golden chance minutes to the end when a cutback from the left landed on his path from good shooting range, but he sent the effort over the bar.
On the other end, Wydad made offensive changes to try and keep the score within good distance, but none of the two sides could notch a goal.
By Brian Mboh