Combative defender Gomaa and Angolan striker Flavio struck home in the first 15 minutes as Ahli claimed a convincing win.
The Red Devils, who share with arch-rivals Zamalek the record of five Champions League triumphs, moved close to winning an unprecedented sixth title.
Nine-time Cameroonian champions Coton will need to spring a huge surprise in the second leg if they are to win their first ever continental title.
Coton were no match for the powerful Ahli, who dominated the entire first half.
Ahli almost opened the scoring after three minutes when classy playmaker Mohamed Abou-Treika released Mohamed Barakat with a deft through pass.
Barakat went clear on goal but Coton keeper Kassaly Daouda rushed out to block his low shot.
But the hosts made amends few moments later as the sell-out crowd erupted into ecstasy.
Gomaa escaped his marker at the near post to head home Abou-Treika's curling free kick from the left.
The in-form Flavio doubled the lead on the quarter hour mark after capitalizing on some sloppy defending from the visitors.
He was found unmarked by Ahmed Hassan's free-kick from near the halfway line. His exquisitely directed back header eluded Daouda.
Ahli still had the better possession afterwards but they slowed down quite a bit.
Their approach helped Coton create a couple of half-chances but Ahli were not bothered.
Squandered Chances
The second half was no different from the first, with Ahli remaining the superior force. The Cairo giants might be blamed for failing to extend the gap.
They wasted two glorious opportunities that could have made their task in the second-leg a walk in the park.
Barakat raced down the right flank before sending in a low cross. Flavio's clever dummy left Abou-Treika in space but his right-footed shot from inside the area went just wide.
Eight minutes from time, Flavio spurned another clear-cut chance.
Abou-Treika's low cross evaded Daouda and found the former Petro Atletico man, who fired astonishingly wide with the goal gaping.
Coton would be satisfied that Ahli hadn't won by a larger margin to keep their slight hopes alive.