Kalisz trailed top qualifier Carson Foster at the midway point of the race after the butterfly and backstroke legs.
But Kalisz surged to the lead on the breaststroke and held it to the end through the freestyle, winning in 4 minutes, 9.09 seconds.
“I know where I need to be to make my move off the breaststroke,” the 27-year-old said.
Phelps, the retired in 2016 after winning a record 23 gold medals at the Olympics, said everyone at the trials should get a boost from racing before fans.
USA Swimming allowed roughly 50% capacity in the 14,000-seat arena, with cardboard cutouts occupying many of the empty seats.
Still, after more than a year without any fans in the stands, the atmosphere was a welcome change for the swimmers.
“You get that electricity from the fans,” Phelps said. “I got goose bumps when I walked into the arena tonight.”
Another 2016 Olympian, Jay Litherland, tracked down Foster over the final 25 meters to claim the expected second spot on the Olympic team in 4:10.33.
Foster settled for third — out of the Olympics — in 4:10.86.
That ensured a couple of veterans were the first swimmers to claim spots on the squad that will head to the pandemic-delayed Tokyo Games with high expectations.
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