Makoni said he decided to run following extensive consultations with party members and activists across Zimbabwe, where Mugabe had been expected to win the election unchallenged by a weak and divided opposition.
"I have accepted the call and hereby advise the people of Zimbabwe that I offer myself as a candidate for the office of President of Zimbabwe in the forthcoming elections," Makoni, a member of the party's politburo and former finance minister, told a news conference.
Speculation has been rife that some party stalwarts would launch a rival party to challenge Mugabe, 83, who is accused by critics of wrecking the southern African country's once promising economy.
Local media reports have suggested the breakaway party would be headed by Makoni and enjoy the patronage of an influential retired army general, Solomon Mujuru, but officials linked to the suspected plan have declined comment.
For years, Makoni -- who is regarded as a reform-minded technocrat -- has been touted as a possible successor to Mugabe. But Makoni's critics say he is a political lightweight with no stamina to fight one of Africa's most combative leaders.
Mugabe, in power since independence from Britain in 1980, is seeking another five-year term after brushing off attempts from top officials in his governing ZANU-PF to force him to retire.
Mugabe has vowed to clinch a landslide victory to silence the opposition and shame Western foes he says are sponsoring his rivals to remove him from power.
Critics say the veteran leader has ruined Zimbabwe through controversial policies such as the seizure of white-owned farms for blacks and lately plans to localise foreign-owned companies, including banks and mines.
Mugabe denies wrecking the economy and blames former colonial ruler Britain for leading a Western onslaught against his government as punishment for the land seizures.