A close-range effort from Egypt talisman Mohamed Salah after four minutes struck the woodwork before hitting Ciss and bouncing back into the net, with the sell-out crowd at Cairo’s International Stadium erupting into ecstasy.
Egypt were then pinned in their own half for long spells as Senegal mounted an onslaught, although clear-cut chances were scarce.
The hosts, who struggled to keep hold of the ball or threaten the Teranga Lions on breakaways, held on for a narrow yet vital win before the second leg takes place in Dakar on Tuesday.
Salah and Liverpool teammate Sadio Mane were largely subdued, although both produced flashes of individual brilliance, more than a month after Mane scored the winning penalty in a shootout win over Egypt in the African Nations Cup final.
Some flying tackles cost both teams, with Senegal losing defender Abdou Diallo early on due to a groin injury and Egypt substituting center-back Mohamed Abdel-Moneim late in the first half after an aerial collision with Mane left him with a bloody nose.
The first half was cagey and physical, with the early opener being one of the few highlights.
Salah displayed his predatory instincts to send the home fans into raptures after just four minutes, escaping the attention of Ciss to superbly control a chipped pass from midfielder Amr El-Sulaya.
He swiveled and rattled the bar with a powerful left-foot shot, with the ball then rebounding off the knee of the unfortunate Ciss and into the back of the net.
Senegal, looking for a quick response, launched numerous crosses from the right as Bouna Sarr and Ismaila Sarr repeatedly combined down the flank to unsettle Egypt’s left-back Ahmed Fattouh.
However, Egypt’s central defenders stood firm, with the three-man midfield dropping deep to clear whatever a vibrant Senegal side throw their way.
Senegal’s only real chance in the first half fell to Mane, who bamboozled Abdel-Moneim and rushed towards the edge of the area unopposed in the 37th minute, only to miss the target with an attempted curler.
Egypt struggled to create openings from open play but they still went close from a set-piece four minutes later, central defender Mahmoud El-Wensh sending a free header high over following a free-kick from Trezeguet.
The second half was a one-way traffic as Senegal piled on pressure. Their promising attacking attempts were denied by some last-ditch interceptions from defenders Omar Gaber and Yasser Ibrahim.
Egypt keeper Mohamed El-Shennawi also made a couple of fine saves, pushing away a header from Mane and smothering an angled shot from the lively Ismaila Sarr at his near post.
The late introduction of Marmoush injected some zeal as Egypt relatively improved in the dying minutes, with the Stuttgart winger hitting the side netting with a shot from a tight angle in a rare chance for the seven-time African champions.