Phelps trailed after the first two legs but took over in thebreaststroke and moved clear in the freestyle to win in 1 minute54.66 seconds.
Japan's Kosuke Hagino, medley winner over 400m was second in 1:56.61with China's Wang Shun taking bronze.
It is Phelps' third gold of the Rio Games and he returns to the poollater Thursday in the semi-finals of the 100m butterfly.