Phelps, competing for the first time this week following a six-month ban for a drunk driving conviction, finished strong over the final 50 meters of the 100 to finish in 49.72 seconds at the Mesa, Arizona meet.
Lochte, who won the 200 individual medley in 1:58.70, finished five-hundredths of a second behind Phelps in the 100 free.
"Tonight was the best night of racing I think I've had since I was here (a year ago)," said Phelps.
Phelps is competing for the first time since last August with an eye toward returning to glory at the 2016 Olympic Games in Rio.
In the 200 individual medley, he finished third, behind Lochte and Conor Dwyer.
Phelps is the most decorated Olympian of all time, with 18 golds and 22 total medals, while Lochte has eleven medals, five of which are gold. - Reuters
