Official results put Mr. Ma, of the Kuomintang party, nearly 17 percentage points ahead of Frank Hsieh of the ruling Democratic Progressive Party. Both candidates advocated closer economic ties with China, but differed over the pace and degree of change.
Mr. Ma pledged to strengthen commercial ties more quickly than Mr. Hsieh, who took a more cautious approach. He will succeed arch-nationalist Chen Shui-bian, who steps down in May.
Over 17 million people were eligible to vote and turnout figures are expected to be high.