Sergio Floccari put the Italians ahead in the 14th minute and the veteran striker scored his second on 37 minutes.
Fotis Papoulis reduced the deficit before half-time but the visitors could not find the equaliser despite having numerous chances.
The result has lifted Lazio to second in Group J, two points adrift of leaders Trabzonspor, who won 2-0 at Legia Warsaw in the other pool game.
Apollon, who held Lazio to a goalless draw in Cyprus two weeks ago, are third, four points behind the Italians with two games remaining.
The hosts enjoyed a strong start and went ahead when Apollon failed to clear Keita Balde's low cross in the area.
That left Floccari unmarked and able to strike a right-footed shot past Apollon goalkeeper Bruno Vale.
Vale was called on to make a good save in the 25th minute to clear Hernanes' 30-yard attempt towards the far post.
Lazio continued to press forward and doubled their lead when Floccari got past his marker and headed Keita's corner-kick towards the far post and out of Vale's reach.
The visitors made it 2-1 in the 39th minute after Lorik Cana's poor clearance allowed Gaston Sangoy to set-up Papoulis in the box.
His diagonal shot beat Lazio goalkeeper Etrit Berisha.
Lazio wasted a great chance to extend their lead three minutes into the second half when Vale failed to hold onto Hernanes' free-kick and Keita shot high and wide from six yards.
Shortly after the hour mark, Sangoy's powerful header went over the bar.
The closet Apollon came to an equaliser was 20 minutes from time when Berisha kept out a 12-yard shot from Papoulis.