For the third time this week, the pair battled each other stroke-for-stroke at the US Olympic trials in America's Midwest, this time in the 200 metres individual medley.
Lochte beat Phelps in the 400m individual medley on Monday but Phelps avenged that loss when he got his hand on the wall first, stopping the clock at one minute 54.84 seconds.
"It feels good to be back on that (winning) side," Phelps told reporters.
"But I'm sure that's not going to be the end of us going back and forth."
Lochte, who had won the 200m backstroke final just 30 minutes before taking on the greatest Olympian of all time, was just 0.11 seconds behind, setting the stage for another epic duel in London when both men will be at their peak.
Phelps has already qualified for four events in London and looks certain to add a fifth after setting the fastest time in the semi-finals of the 100m butterfly.
With the addition of the three relays, he will swim the same eight events he contested at Athens and Beijing.
"It doesn't really matter what happens here, the bigger races are a couple of weeks down the road," Phelps added.
"The next race is the one that counts, I know that, and that's one thing that I'm looking forward to."
Lochte also qualified for the 100m butterfly final after swimming three races in less than hour on Saturday.
The 27-year-old has already clinched his place in four events but unlike Phelps, is not assured of a place in all three relays.
"Tonight was probably the most pain I have endured in a swimming competition," Lochte said.
"Going back-to-back was definitely tough but I was up for the challenge and I've trained for it.
"I know this meet was just stepping stones for what I really want to do in London."
A woman possessed
Teenage sensation Missy Franklin looks set to compete in seven events at her first Olympics after the 17-year-old finished runner-up in the 100m freestyle final and set the fastest qualifying time for Sunday's 200m backstroke final.
Like Lochte, she was back in the pool within half an hour of her previous race and finished second in 54.15, behind Jessica Hardy (53.96), who booked her first trip to the Olympics after being forced to miss Beijing over a doping offence.
Hardy was suspended after testing positive for the banned steroid clenbuterol at the 2008 US Olympic trials. She denied any wrongdoing and fought a long legal case which was only resolved last year.
Driven by raw emotion after missing out in the 100m breaststroke, an event she owns the world record in, Hardy swam like a woman possessed.
"Never in a million years would I have thought I could win that race," she said. "That was pure heart out there."
Natalie Coughlin sneaked in to the team for her third Olympics when she finished sixth in the 100m freestyle final, securing a place in the relay after missing out in her individual events.
"It's a relief," Coughlin said. "This isn't the meet that I visualised or anticipated going into this year, or even into this quadrennium, but right now I couldn't be happier." – Reuters