Lochte was timed in 2 minutes, 1.03 seconds Saturday to lead eight qualifiers into the evening final.
Phelps won his heat in 2:04.16, qualifying fifth in a time that was 3.13 seconds behind longtime rival Lochte. Phelps took the lead on the breaststroke leg after being third on the first lap.
Both Olympians will swim the 100 freestyle heats later.
Another Olympian, Conor Dwyer, was second-quickest in the 200 IM at 2:02.20. Also making the final was Austin Surhoff, the son of former major league baseball player B.J. Surhoff.