The forward hit a screamer from the edge of the box with just two minutes of time remaining to clinch all three points for the Abu Dhabi club.
While most other Pro League clubs play foreigners in the attacking positions, manager Ivankovic took the decision to deploy Al Kathiri as his centre-forward with Papa Waigo and Marcelo Oliveira - his two overseas strikers - on the wings.
And the call paid off.
"I told two days ago Saeed has worked very hard over the summer and his goal was the kind of reward," Ivankovic said. "I am very proud of him. Saeed didn't get a regular place in the line-up last season but he has already impressed everyone with his performance so far."
The 24-year-old Al Kathiri has three goals from three starts this season after a brace against Al Nasr in the Etisalat Cup opener. He also netted for the UAE in the 3-0 win over Kuwait in a friendly on September 11.
Ivankovic felt his side deserved the victory.
"It was our first game at home and the result was very important," the Croatian said. "We created a lot of chances in the first half but we didn't have the luck. Two shots hit the post and I thought the players were also a bit nervous and missed a lot of scoring opportunities.
"Shabab was a good team last season and they had retained most of their players. So we expected a hard game. But we were the better team and I am proud of my players because they never gave up until the end. They played at the high level for all 90 minutes.
"Sometimes we get punished when we create chances and can't score but I am glad that didn't happen tonight. I would have been gutted if we didn't win."
Wahda were unlucky in the first half, hitting the woodwork twice. First it was Marcelo's effort from 25 yards and then Al Kathiri's bullet from 35 yards.
Marcelo also missed a golden opportunity to put the home side ahead shortly before the break. Matar set him up inside the box and he had only Ismail Rabee, the Shabab goalkeeper, in front of him. However, a meek effort from the Brazilian saw the ball take a slight deflection and roll past the far post.
Wahda's misfortunes continued into the second half as Hamdan Al Kamali's fiercely-struck low free kick was instinctively cleared by Rabee' foot.
The pressure was beginning to tell on the home side as they misplaced passes and lost possession frequently in the final quarter before Al Kathiri's super finish to give them their first points in the league.
Tawfeek Abdulrazaq set him up and the forward sent a vicious shot past a diving Rabee into the corner of the net.
Marcos Paqueta, the Shabab coach, thought it was an even game.
"We played a good game," the Brazilian said. "We created some chances but we couldn't convert them in to goals. It was a 50-50 game and Wahda managed to score at the end and win the game."
Al Wahda 1 Al Shabab 0
Al Wahda Al Kathiri 88’
Man of the match
Ismail Matar (Al Wahda)
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