Michu looked to have put the home side on course for a third straight Group A win when he grabbed his sixth goal of the season, and fourth of this European campaign, by sliding the ball beyond Aleksandr Belenov in the 68th minute.
But the visitors snatched a point when Swans keeper Gerhard Tremmel brought down substitute Ibrahima Balde, and former Liverpool forward Cisse calmly scored from the spot.
The result means Swansea remain top of Group A and move on to seven points, but this was a distinctly unimpressive display from the Welsh club against a limited opponent with just one win from their previous nine games.
Valencia's romp to a comprehensive victory over St Gallen in tonight's other group fixture moves the Spanish team onto six points, and Swansea have plenty of work to do to reach the last 32.
There had been few bright points during a tepid first half, but the hosts would have led had Jonjo Shelvey kept his composure.
Michu's first-time pass found the midfielder in acres of space, but his rushed shot was nowhere near finding the target.
Wilfried Bony volleyed over and Shelvey prodded wide from rare examples of incisive Swansea play, while at the other end Tremmel shovelled Maksim Zhavnerchik's drive wide and Dwight Tiendalli was fortunate to escape a red card after hauling down Lorenzo Melgarejo.
The hosts finally found some control after the break, with Michu making another telling intervention by racing onto a smart Alejandro Pozuelo pass to beat Belenov as he raced from his goal.
But they were pegged back in injury time after Tremmel brought down Balde having delaying his decision to come out to meet the striker, and Cisse made no mistake.
Source: PA
Source: PA