The GFA, which said on Wednesday it had solved a row over player appearance fees, confirmed the decision on its website (www.ghanafa.org) ahead of the team's Group G game against Portugal in Brasilia on Thursday.
Ghana lost the match 2-1 and were eliminated with one point from three matches.
Boateng was sanctioned following "vulgar verbal insults targeted at coach Kwesi Appiah during the team's training session in Maceio this week," the GFA said.
Muntari's suspension was handed down "in the wake of his unprovoked physical attack on an executive committee member of the GFA and a management member of the Black Stars, Mr. Moses Armah, on Tuesday 24th June, 2014 during a meeting."
Muntari had punched Armah during a meeting over the unpaid money as senior players rounded on team officials for not keeping promises, a team source added.
Boateng had shown "no remorse for his actions" and both players had their World Cup accreditation withdrawn.
Boateng denied swearing at the coach but said he accepted the suspension and wished his colleagues well for their last Group G game.
"No one should think that I insulted the coach or did anything wrong," he told the website of German's Sport Bild magazine (www.sportbild.de).
"Yesterday, there was an incident during training. Sulley Muntari and I had a joked over a duel. I said that he had handled the ball. He said 'no'. Then I laughed and said: 'Hey, you're the referee or what?' Then we both laughed. The coach stopped the training and asked why we were laughing? We said that everything was okay. He then sent me to the changing room.
"After training I went to the coach and asked him if he had a minute for me. I asked him what he had against me? Then he started yelling at me. He insulted me."
Ghana missed training in Brasilia on Tuesday because of the row over fees, with the players conducting a series of meetings to discuss the matter and the nation's president, John Mahama, later stepped in to try to resolve the dispute.
Appiah said a consignment of money was on its way to the Brazilian capital by plane and that cash was required as many of his squad did not have bank accounts in Ghana.
The coach also said the situation had left him suffering many sleepless nights and should have been sorted long ago.
Appiah, speaking at a news conference, did not rule out a return for the pair and said discipline came first.
"The decision was taken the day before the match, it's just that it came out the morning of the match," he said.
"Sometimes, you have to make decisions which are for the benefit of the whole team.
"The letter (to them) said it was just suspension so if they are performing well they could be invited back to the team."
Muntari was set to miss the Portugal game as he was suspended after earning a second booking of the tournament in last week's 2-2 draw with Germany.
This is the second time Ghana have expelled Muntari from a major tournament for disciplinary reasons. He was sent home just before the 2004 Olympic Games in Athens for breaking a curfew and did not play for Ghana for almost two years until just before the 2006 World Cup finals in Germany.
In 2010 he was left out of the squad for the African Nations Cup finals in Angola for disciplinary reasons and last year had to write an apology letter to coach Appiah after he swore at him after being substituted during a World Cup qualifier against Lesotho.
Boateng was enticed by the prospect of playing for Ghana at the 2010 World Cup and committed his international career to the Black Stars ahead of Germany, where he was born and for whom he played at junior level.
But he 'retired' from the national team within 18 months, citing club and family pressures but seemingly less than enthralled by the prospect of leaving his then club AC Milan in mid-season to play at the 2013 African Nations Cup finals.
Last August, the 27-year-old Boateng announced he was making himself available again for selection at the same time as Ghana were comfortably on course for World Cup qualification.
- Sports & Recreation
- Sulley Muntari
- Kwesi Appiah