In the day's other first-leg semifinal, another eight-time champion, Dhofar, beat Al Nahda 1-0 at the Sohar Sports Complex, courtesy a 59th minute goal from Ahmed Mani.
At the SQSC, all three goals came in the first half, with Fanja's Senegalese striker Cisse scoring on either side of Milod Nakhli's lone strike for Bausher.
Fanja fans were not deterred by the persistent rain and turned up in considerable numbers. Some of them held out a massive banner that read 'Make it No 9’, referring to Fanja’s pursuit of winning the tournament a record nine times.
The Fanja players didn’t disappoint their fans though. They found their first clear chance in the tenth minute when a free-kick taken by Abdulaziz al Miqbali from just outside the penalty area hit the left post.
It didn't take long for Fanja to take the lead. Cisse found the opening goal on a drizzling night in the 14th minute. He expertly collected the ball from just outside the penalty area and lobbed it into the net.
Bausher equalised in the 28th minute when Nakhli headed in a cross from the right, setting up an interesting contest.
But it didn't take long for Fanja to win back the initiative. Ahmad al Mukhaini was fouled on the edge of the penalty area in the 33rd minute. Mukhaini took the free-kick, curling the ball for an onrushing Cisse to head it in and make it 2-1.
Quite expectedly, Fanja began the second half looking to defend its lead and the Bausher attack tried to make inroads, desperate for an equaliser.
Two minutes before the hour mark, Fanja was reduced to ten men when its defender Basil al Rawahi was sent off after collecting his second yellow card of the night. The sending-off, however, didn’t affect Fanja's intensity as it kept on defending and keeping the Bausher forward line at bay, even making the occasional inroad into the opponent's half.
Bausher was reduced to ten men three minutes from regulation-time after Ahmed al Shibli was sent off following a double booking.
The second-leg semifinals are slated for May 3.