Flares and fireworks ripped into the skies above Bosnia's capital, Sarajevo, and other cities as the former Yugoslav republic finished top of Group G, level on 25 points with Greece but ahead of their more heralded rivals on goal difference.
After several narrow failures in the past, Bosnia seemed to be heading for another play-off as a packed Lithuanian defence, headed by inspired goalkeeper Giederius Arlauskas, frustrated the visitors before Ibisevic struck midway through the second half.
Keeper Asmir Begovic did well to keep out a Kalonas Mindaugas shot in the 77th minute and Bosnia held firm in a nervy finish to book their place in the 2014 finals, their first major tournament since the country declared independence in 1992.
Greece will have to negotiate a two-legged play-off if they are to reach Brazil as their 2-0 home win over Liechtenstein could not prevent them finishing behind Bosnia.
Dimitris Salpigidis finished off a neat passing move while skipper Giorgos Karagounis curled home a free-kick to produce two rare moments of quality in an otherwise tepid encounter as Bosnia's 1-0 win in Lithuania proved decisive.
Both teams ended qualifying with 25 points but Bosnia's superior goal difference saw them qualify for the World Cup for the first time in the country's history. Greece will have to wait to see if they can make what would be their third appearance in the competition.
In the group’s late kick-off, Latvia’s Renars Rode struck an injury equaliser as they fought back from two goals down to force a 2-2 draw with Slovakia.