Football's world and European governing bodies had asked Bosnia's football federation (NFSBiH) to replace the current system for the presidency, under which a Serb, a Croat and an ethnic Muslim take turns in holding the post, with a single leader by March 31.
The NFSBiH congress rejected a motion that would meet that request this week, triggering the suspension.
It means Bosnia may not be able to continue playing their Euro 2012 qualifiers, though FIFA and UEFA said they would meet soon to discuss how to bring the country back into the international fold.
"The NFSBiH representative and club teams are no longer entitled to take part in international competitions as of 1 April 2011 and until the... problem is solved," FIFA and UEFA said in a joint statement.
"FIFA and UEFA deeply regret that this decision had to be taken and will meet shortly to discuss the next steps required to try to bring NFSBiH back into the football family as soon as possible."
NFSBiH secretary general Jasmin Bakovic said the federation's problems reflected wider political problems in Bosnia.
"We are simply a part of the general society and the NFSBiH is just a mirror image of the state," Bakovic told Reuters.
"In this country, if you don't meddle with politics, then politics will meddle with you.
"The worst-case scenario would be to have the suspension extended until the end of the year and that would certainly have catastrophic consequences."
NEXT STEPS
Bosnia's hopes of continuing to play for a place in next year's European Championship finals effectively rest on them have the suspension overturned before their next scheduled qualifier, away to Romania on June 3.
They are currently fourth in Group D, five points behind leaders France and a point behind Belarus and Albania but with a game in hand on all three.
The group winners qualify automatically for the finals in Poland and Ukraine, with the second-placed team retaining a chance of going through either from a playoff or as the best of the runners-up.
Radmilo Sipovac, president of Bosnian first division leaders Borac Banja Luka, said the suspension might be a blessing in disguise.
"The FIFA and UEFA decision may be good because it could persuade the people who have obstructed Bosnia's soccer for years to leave," Sipovac said.
Sipovac added that he expected urgent action by Bosnian officials to resolve the problem.
"I expect an urgent formation of an interim body that would pass statutes fully in line with FIFA and UEFA requirements," he said.
"It would be irreparable damage for Borac to be left out of European competition now that we are so close to winning the league title."
Bosnia coach Safet Susic, speaking to Reuters by telephone, said UEFA should impose a solution that would lift Bosnia's suspension.
