Jazira, who started the cup campaign late due to their Super Cup involvement, edged past a determined Baniyas side.
Etisalat Cup: Baniyas 2 Al Jazira 3
Subait Khater gave them the lead before Salem Masoud struck twice early in the second half.
Yousuf Jaber had cancelled Jazira's lead with a penalty in added time in the first half.
Nawaf Mubarak reduced the deficit with a stunning left-foot shot from just outside the box in the 73rd minute to set up a thrilling finish and Andre Senghor had a chance to clinch a share of the spoils in injury time but his header crashed against the bar.
Jazira got the opener when Ricardo Oliveira crossed from out wide and Khater timed his run on the far side of the post to perfection to connect a neat header.
Baniyas pressed hard for the equaliser and were rewarded with a penalty, which Jaber converted with a powerful strike to the corner of the net.
Adnan Hussain, chasing a high ball from Jaber, was felled by Mohammed Bargash and the referee Mohammed Al Zarouni had no hesitation in pointing to the spot.
Senghor had two scoring opportunities earlier. The Senegalese forward was off target with a shot from inside the box and just failed to lob the ball over the charging Jazira goalkeeper, Ahmed Al Shabibi.
Paulo Bonamigo, the Jazira coach, strengthened his attack in the second half by bringing on the Brazilian forward Fernandinho in place of Ahmed Mohamed.
It worked for them as they regained the lead through Masoud, who tapped in a rebound after Mohammed Khalef, the Baniyas goalkeeper, had blocked a free kick from Khater.
Masoud then headed a long ball from Sultan Bargash for his second goal within five minutes.
And it could have been three goals in 10 minutes had Oliveira's effort not crashed against the post.
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