Leverkusen, who have now won four straight games in all competitions, move to 18 points, two ahead of champions Borussia Dortmund who are fifth after their goalless draw against VfB Stuttgart on Saturday.
Bayern Munich notched their ninth win in 10 games, beating Hamburg SV 3-0 on Saturday to go seven points clear at the top with 27. Sidney Sam was sent through by Stefan Kiessling to chip in for the lead after a quarter of an hour as Fortuna, who have now lost four league games on the trot, initially boxed themselves in.
They did grab an equaliser through Nando Rafael's deflected header off defender Omer Toprak in the 40th but had only 40 seconds to celebrate as Andre Schuerrle, who had earlier rattled the crossbar, thundered the ball in from six metres to hand Leverkusen back the lead.
The hosts suffered another setback when substitute Simon Rolfes got his marching orders two minutes after coming on in the 66th for a hard tackle from behind on Adam Bodzek. But they instantly bounced back again with Gonzalo Castro tapping in only a minute later from close range after Daniel Carvajal made the most of a Fortuna mistake to set up his teammate.
Bodzek drilled in from 24 metres out four minutes from time to set up a nervous finale but the visitors, despite scrambling forward, eventually ran out of time. Schalke 04 slumped to a last-gasp 3-2 defeat against Hoffenheim on Saturday to stay second on 20 along with third-placed Eintracht Frankfurt who drew 1-1 against Greuther Fuerth on Friday.
(Reporting by Karolos Grohmann; Editing by John Mehaffey)