Morgan Tsvangirai, 65, a former Zimbabwean prime minister, is receiving medical treatment in South Africa as he battles cancer of the colon.
Tsvangirai has led the MDC since its formation in 1999 and the party has posed the most formidable challenge to the ruling Zanu-PF.
The announcement comes amid reports of jostling for leadership of the party among the three MDC-T vice-presidents who include Thokozani Khupe and Elias Mudzuri.
Tsvangirai's spokesperson Luke Tamborinyoka said in a statement the former union chief had appointed Nelson Chamisa, 40, as acting president "until the president's return".
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Tsvangirai, 65, has been the MDC's figurehead since the party was founded almost 20 years ago.
But since signing up to the loose merger previous year, political parties to the anti-Zanu PF front have vowed support for Tsvangirai's continued leadership even in his current state of health.
General elections were due to be held in September in Zimbabwe, and the MDC Alliance had confirmed that Morgan Tsvangirai would be their presidential flag bearer in the forthcoming presidential elections.
The appointment was widely construed to suggest the embattled MDC-T leader has finally ordained his youngest deputy as successor.