"It wasn't a perfect race, but the good thing was that I won and I came out injury free," said Bolt, who got away slowly but powered home, catching the field at about 50 meters and celebrating as he got to the line first to the delight of a big crowd at the national stadium in Kingston.
The sprint superstar led three compatriots under 10 seconds in a race run in a wind of one meter per second.
The race was only the fourth time that Bolt, former world record holder Powell and 2011 world champion Yohan Blake have clashed in Kingston and more than 30,000 fans turned out for the warm up for Jamaica's Olympic trials later this month.
Powell had hoped for better, running fourth despite what he described as a calf cramp.
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Running before his home crowd for the first time in about two years, Bolt said: "It's good to be back, it has been a while since I ran here."
"Even when you don't get it right you have to stay strong, composed and run through," he said.
"I was not completely happy with execution as the start was horrible and did not set up the race, but I won and that is good."
Bolt improved on the 9.98sec he posted in Ostrava on May 20.
With the August 5-21 Rio Games less than two months away, Bolt moved ahead of US rival Justin Gatlin on the 2016 world list, the American owning a time of 9.93 that puts him fourth-fastest in the world this year.
American Barbara Pierre was second in 11.11 and Trinidad
and Tobago's Kelly-Ann Baptiste took third in 11.15 seconds.
In other events, Shauna Miller of the Bahamas ran a personal best 22.05sec to win the women's 200m.
The lanky runner came off the curve in second place but chased and caught American Jenna Prandin and eased away to win her second half-lap race in Kingston this year.
Prandin clocked 22.39 seconds while Jamaican Audra Segree was third in 22.89 seconds
Jamaica's Julian Forte was second in 20.18 ahead of compatriot Warren Weir, who settled for third in 20.32.
American Johnny Dutch won the 400m hurdles in a world leading 48.10sec, surpassing his own 48.6 set on April 16th in the Bahamas.
Jamaican Roxroy Cato was second in 48.98 seconds and Annsert Whyte of Jamaica third in 49.25.
South Africa's 400m world champion Wayde Van Niekerk, won the rarely contested 300m in a blistering 31.03sec.
US 400m threat LaShawn Merritt was second in 31.23, and Tony McQuay third in 31.64.