Lochte, who beat Phelps for the world title in the event in Shanghai last year, qualified fastest, winning his heat in 1:48.14.
Charlie Houchin had the second quickest time of the morning of 1:48.15 and Phelps, the reigning Olympic champion and former world record-holder, was third fastest – winning his heat in 1:48.31.
Lochte opened the eight-day meeting, where the top-two finishers in each final secure spots in the team for the London Games, with a triumph over Phelps in the 400m individual medley on Monday.
Phelps finished second to secure his Olympic berth and the 14-time Olympic gold medallist said he was pleased to get that formality – and the demanding 400m IM – out of the way.
"This morning felt pretty comfortable, so hopefully we can just keep everything rolling for the rest of the meet," Phelps said. "Definitely happy with getting last night out of the way early."
Phelps's decision to return to the 400m medley after dropping it from his regular programme in the wake of the Beijing Games sets him up to go for eight medals in London.
Whether he could match his unprecedented eight-gold haul of Beijing, Phelps said: "Anything can happen. You've got to be in the right place at the right time."
New and improved
This time around Phelps must contend with a new and improved Lochte, who is eyeing his own set of multiple medals.
Shortly after the 200m free heats, Lochte returned to the pool and posted the second fastest time behind Matt Grevers in the 100m backstroke heats.
"It wasn't that bad of a double, the 100 back hurt worse than the 2-free," he said. "The 2-free felt really smooth."
Lochte – who entered a whopping 11 events – promptly scratched from the semifinals of the 100m back.
Missy Franklin, the 17-year-old Colorado high school student tipped for Olympic stardom after a breakout performance at the 2011 World Championships, led the way into the semifinals of the women's 100m backstroke in 59.54.
Rachel Bootsma (18) was second quickest in 59.69, followed by 18-year-old Elizabeth Pelton and 17-year-old Olivia Smoliga.
Behind the youth brigade, 29-year-old Natalie Coughlin was the fifth-fastest qualifier, clocking 1:00.71 as she took a first step to defending the gold medal she won in both Athens and Beijing.
What's at stake
Franklin got a mid-race reminder of what's at stake in Omaha the "United States Olympic Team" sign stretched across the bottom of the massive electronic scoreboard hanging over the pool.
"Talk about motivation," beamed the winner of three gold medals at the World Championships in Shanghai last year.
"It helped get my tempo up in the last 25. I was nervous for my first race. But right now, I feel good."
World champion Rebecca Soni led the way into the 100m breaststroke semi-finals with a time of 1:06.33. Unheralded Breeja Larson was second-fastest in 1:06.52 and Jessica Hardy, who won the event at the 2008 trials but lost her Olympic spot because of a failed drugs test, was third-fastest in 1:07.25.
Hardy served a one-year ban after arbitrators agreed with her claim that her positive test resulted from a tainted supplement.
Amanda Beard, the 1996 Olympic silver medallist, posted the morning's seventh-fastest time to reach the semifinals.
Allison Schmitt led the way into the women's 400m freestyle final ahead of Kathleen Ledecky and Chloe Sutton. American record-holder Katie Hoff failed to qualify, managing just the 20th-fastest time.– Sapa-AFP