Lochte followed up his victory over Phelps in Monday's 400 individual medley when he easily won his 200 heat in one minute 48.14 seconds, while the Olympic champion was relegated to third in 1:48.31. The top 16 qualified for the semi-finals.
Lochte also qualified second fastest behind Matt Grevers in the 100 backstroke preliminaries, but scratched himself from the semi-finals because of his heavy programme.
"The 100 back hurt worse than the 200 free," said Lochte, who swam the two heats about an hour apart. "The 200 free just felt really smooth."
Lochte and Phelps have both entered multiple events but neither has confirmed exactly how many they intend to swim at the Olympics.
"It's not an easy programme, but we're going to try to do some things here," Phelps said.
"The biggest thing is really how I hold up all week. I was definitely happy with getting last night out of the way early.
"It wasn't the easiest race but this morning felt pretty comfortable, so hopefully we can just keep everything rolling for the rest of the meet."
Missy Franklin, the emerging star of the American women's team, set the pace in the women's 100 backstroke when she touched the wall in 59.54 seconds.
The 17-year-old from Colorado admitted to suffering from a bout of nerves before the first of her five events but was full of energy once she got in the water.
The only other woman to break a minute was Rachel Bootsma while Natalie Coughlin, who won the 100 backstroke at the past two Olympics, was fifth overall.
"It was such an adrenaline rush," said Franklin.
"I had some first-race jitters but I'm super, super happy with my time.
"It felt so good to get that first race out of the way."
World champion Rebecca Soni set the fastest time in the women's 100 breaststroke heats, stopping the clock at 1:06.33, while world record holder Jessica Hardy was third and Amanda Beard, who is bidding to qualify for her fifth Olympics, was seventh.
There was more disappointment for Katie Hoff when she failed to qualify for the final of the women's 400 freestyle. Seeded third, the 2008 Olympic silver medallist, could manage 20th place only.
She had earlier withdrawn from the 400 individual medley, in which she twice held the world record.
Janet Evans, the former Olympic champion and world record holder in the 400 freestyle, also failed to qualify for the final.
The 40-year-old, who won gold medals at Seoul in 1988 and Barcelona four years later, retired after the 1996 Atlanta Olympics but decided to make a comeback in the hope of making it to London.
She had defied the odds just by qualifying for the trials in both the 400 and 800 but finished seventh in her heat and 80th overall, nearly 16 seconds behind the fastest qualifier, Allison Schmitt.
"I wish I'd gone faster," Evans said. "It's not what I wanted but it is what it is. I think the 800 will be better."
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