The American touched in 1min 54.11sec, fastest in the world this year. He finished a body-length ahead of Australia's Nick D'Arcy, who was timed in 1.54.73 after coming into the final with the world's fastest time.
Takeshi Matsuda of Japan was third and China's Peng Wu fourth.
"The last 50 hurt," said Phelps, still breathing hard minutes after the race. "I was just like, `Please, get to the wall.' I felt the splash of water in the lane next to me, and I was like, `Please, don't get run down.' The fitness level is just not there."
He may not be in the same form that earned him a record eight gold medals at the 2008 Olympics, but it was Phelps' 31st consecutive victory in a 200 fly final. He has not lost since American Tom Malchow beat him at the 2002 Pan Pacs.
"That was the race I really came on the scene in," he said. "I do like coming out and racing it."
American Ryan Lochte cruised to victory in the 200 freestyle with the fastest time in the world this year.
Lochte touched in 1.45.30 wearing a waist-to-knee "jammer" textile suit that was mandated earlier in the year. Olympic silver medalist Park Tae-hwan of South Korea was second in 1.46.27, narrowly ahead of American Peter Vanderkaay, the bronze medalist in Beijing.
Olympic champion Aaron Peirsol won the 100 backstroke in 53.31, bettering his own meet record of 53.32. He took advantage of Lochte dropping out of the final after the morning preliminaries. Lochte and David Plummer were the fastest Americans and only two swimmers from each country make the finals, so that left Peirsol out.
Lochte only wanted to swim the 100 back once at this meet, so he scratched the final.
"I'll get him a beer when the meet is over," Peirsol said.
Peirsol was fourth at the turn, then poured it on down the stretch to win in his hometown pool. Junya Koga of Japan was second in 53.63. Ashley Delaney of Australia was third.
"No-one will just leave me alone in that race," Peirsol said. "The world is getting very fast. I still love this race. It's just me trying to fend off 20 people instead of three, which isn't easy. I haven't really put up a competitive world time this year."
Cesar Cielo of Brazil won the 50 butterfly with the world's fastest time.
Cielo, the world and Olympic champion in the 50 freestyle, touched in a meet-record 23.03sec. He defeated team-mate Nicholas Santos, who was timed in 23.33.
"I'm not really a 50-metre butterflyer, but everything that's a 50 I find a way to go fast and tonight I found a way to go really fast," Cielo said. "It was a wonderful surprise."
South Africa's Roland Schoeman (30) was third in 23.39.
Geoff Huegill of Australia, at 31 the oldest man in the final, was fourth in 23.42. He lowered the meet record with a time of 23.27 in the morning preliminaries.
Huegill retired after the 2004 Athens Games, then began a comeback in 2007.
Emily Seebohm of Australia, who at 18 is 10 years younger than two-time Olympic champion Natalie Coughlin, rallied from third to win the 100 backstroke in 59.45. That lowered Coughlin's eight-year-old meet record of 59.72.
Aya Terakawa of Japan was second in 59.59 and Coughlin finished third in 59.70. The top three were the only women under 1 minute in the final.
"When I saw Natalie at 75 metres, I said, `I can't let her win'," said Seebohm, who never had before beaten Coughlin, who led at 50 metres when the Australian was third.
Coughlin took an 18-month break after Beijing and returned to training only in January.
World champion Marieke Guehrer, of Australia, won the women's 50 fly in 25.99, tying the meet record set in the consolation final.
The US went 1-2 in the women's 200 freestyle. Olympian Allison Schmitt won in 1.56.10 - second-fastest in the world this year - and lowering the meet record that Morgan Scroggy had set in the morning heats. Scroggy finished in 1.57.13.
The American women controlled the 800 free, too. Kate Ziegler, world champion in 2005 and '07 who had fallen off in recent years, won in 8.21.59. Chloe Sutton was second in 8.24.51.
Ryan Cochrane of Canada won the 1500 free in 14.49.47, fastest in the world. Chad La Tourette of the US was second and Zhang Lin of China third. World and Olympic champion Ous Mellouli of Tunisia was last in the timed final.
World champion Jess Schipper of Australia edged American Teresa Crippen to win the 200 fly. Schipper, the Olympic bronze medalist, touched in 2.06.90 from lane seven.
