The Czech full-back netted from a late volley as hosts took the spoils and kept a clean sheet, earning their first points of the Bundesliga season after losing their opener
It took 85 minutes for the home side to break the deadlock in what was a rather pedestrian match, but Michal Kadlec finally struck to lift Robin Dutt's side to victory.
Leverkusen looked the better team in the first-half, but easily the best chance belonged to Bremen's Lennart Thy. In the 36th minute, the 19-year old was set up with an open goal, but he looped his shot well over the bar.
Thy's effort came from one of very few opportunities the visitors earned. Leverkusen, though lacking a bit of pace and urgency, managed to carve out a number of chances. Renato Augusto's 18-yard drive forced a superb diving save from Tim Wiese on 13 minutes, and on the stroke of half-time, Stefan Kiessling was denied with only the goalkeeper to beat.
After the break, Andre Schurrle grew in influence for the hosts, but his hard running was not matched by his team-mates. The Germany international had a 20-yard attempt fly wide on 65 minutes, and later have another long-ranged blast miss narrowly over the bar.
With four minutes remaining, the hosts finally made their breakthrough. Following a corner, Kadlec had his header blocked by a team-mate before Simon Rolfes played the ball back into his path. The Czech made no mistake with his second chance, volleying home off the inside of the post.
Eren Derdiyok had a chance to put the game to rest in injury time, but struck the ball straight at Wiese, who saved. The hosts nonetheless managed to hold on for three points.
The result sees Leverkusen join seven more teams - including Bremen - level on three points. Werder are just ahead of their opponents, having earned a +1 goal difference overall, two better than Leverkusen.