The result lifted Bosnia two places up to third with 10 points from six matches, two behind second-placed Belarus who have played a game more after beating Luxembourg 2-0.
Leaders France have 13 points from six matches, while Albania, who have eight points from six games, dropped one place down to fifth behind Romania on goal difference.
The Bosnians enjoyed much of the possession in the first half but failed to create any clear-cut chances against a packed Albanian defence.
Lively playmaker Zvjezdan Misimovic had several long-range efforts blocked while central defender Emir Spahic glanced a header across the face of goal.
The home side pressed forward after the interval and Misimovic had keeper Samir Ujkani at full stretch while striker Edin Dzeko, who had a quiet game, headed wide from close range before Medunjanin finally broke the deadlock on 67 minutes.
Defensive midfielder Boris Pandza floated a long ball down the middle and Medunjanin took it in his stride superbly to steer it into the bottom left corner.
Albania's second-half substitute Andi Lila was sent off in the 87th minute for a reckless tackle on Elvir Rahimic and the visitors were soon punished after they were caught out on the break.
Wing-back Maletic raced clear from his markers after a delightful through ball and beat Ujkani with a crisp low shot from just inside the penalty box in added-time.
