President Museveni has promised to "work closely" with Maj. Gen. (Rtd) Evariste Ndayishimye, who was sworn-in on Thursday as the new president of Burundi.
Mr Museveni said that he's hopeful that the new leader will have a successful tenure in office to ensure continued peace, progress and prosperity of Burundi.
"The resounding victory was a clear manifestation of the level of trust and confidence the people of Burundi have in the new President and his party.
I also thank the people of Burundi for being peaceful during and after the election," Mr Museveni tweeted.
At a stadium in the capital Gitega where the crowd was dressed in identical outfits, Mr Ndayishimiye pledged to "devote all my force to defending the superior interests of the nation and ensure the national unity and cohesion of the Burundian people, peace and social justice."