Ma made the statement while touring south Taiwan, which was hit Aug 8 by the storm that left at least 461 people dead and 192 missing.
The Taiwan government held a news conference to formally announce its approval of the visit of the Tibetan spiritual leader.
The officials from three southern Taiwan counties and cities invited the Dalai Lama to visit Taiwan from Aug 31 to Sep 3 to hold prayer meetings for the typhoon victims and bless the survivors.
"The Dalai Lama is very happy to visit Taiwan," Dawa Tsering, the Dalai Lama's representative in Taipei, said on Wednesday.
In December 2008, Ma had said the time was not ripe for the Dalai Lama to visit Taiwan, apparently for fear of hurting improving relations with China.
The Dalai Lama, in exile in India since 1959 following an abortive uprising against China's invasion of Tibet, has close ties with Taiwan. He has some 500,000 disciples on the island and opened his representative office in Taipei in 1998.
He drew large crowds when he visited Taiwan in 1997 and 2001 to lecture on Buddhism.
The Dalai Lama has lived in India since fleeing China in 1959 after a failed uprising against Communist rule over Tibet. His government-in-exile is not recognized by any country.
