The office of Yoweri Museveni, the Ugandan president, had previously said Sudan would be represented by other government officials.
Sudan reacted angrily to that announcement, demanding an apology from Uganda and calling on the AU to move the summit to another venue.
War crime charges
Al-Bashir is wanted by the International Criminal Court (ICC) on charges of ordering mass murder, rape and torture in the country's western Darfur region.
He has denied the charges but has restricted his travels since an arrest warrant was issued for him in 2009.
In July last year, the AU said its member nations would not co-operate with the ICC in arresting or extraditing al-Bashir.
The president has travelled to Ethiopia, Eritrea, Zimbabwe and countries in the Middle East, including Qatar and Egypt, since the arrest warrant was issued.
Uganda has signed up to the ICC, but has said it respects the AU position with regard to not co-operating on the al-Bashir case.
In July last year, al-Bashir decided not to travel to Uganda for an economic conference after he was warned he could be arrested on war crimes charges.
At the time, Sudanese state media and Ugandan newspapers reported that Museveni had called al-Bashir to apologise for comments from a junior minister that Kampala might arrest him if he attended the meeting.
South Africa said last month that al-Bashir had been invited to the World Cup in Johannesburg along with the rest of Africa's leadership, but the president said his country would be obliged to arrest him if he took up the invitation.
Al-Bashir was sworn in for another term as leader last month after winning an election marred by boycotts by the opposition.
He was indicted by the ICC in March last year over his alleged role in the Darfur conflict, which the United Nations says has left up to 300,000 people dead, with an estimated 2.7 million displaced.
Khartoum disputes the figures saying that only 10,000 people have died since fighters rose up against the government and its allies in 2003.