The 20-year-old McEvoy of Australia won in 47.82 seconds in rainy conditions Friday night at the Gold Coast Aquatic Centre's outdoor pool, edging Olympic champion Nathan Adrian of the United States into second place at 48.30 and world champion James Magnussen into third at 48.36.
Phelps, the 18-time Olympic gold medalist, opened his program in the morning heats and qualified third fastest, and went marginally slower at 48.51 in the night final.
Elsewhere, Australian sisters Cate and Bronte Campbell finished 1-2 in the women's 100m, with Simone Manuel earning her first international individual medal when she held off US teammate Missy Franklin for bronze. Cate Campbell swam the fastest time of the year to qualify fastest for the final in 52.62 seconds, and went a shade slower to win the gold at 52.72.
In the earlier 100 breaststroke finals, former 50 breaststroke world champion Jess Hardy won her first Pan Pac title over the 100 when she touched in one minute, 7.74 seconds, beating Kanako Watanabe of Japan by four-hundredths of a second.