Bolt won in a time of 20.03sec in an unfavourable headwind in his last outing before he defends his sprint titles at the world championships in Daegu, South Korea, from August 27.
The Jamaican superstar came into the straight comfortably ahead to celebrate his first career victory in the Swedish capital after two previous failures over 100m.
"It's fantastic to record my first win here," said Bolt, who admitted he had felt a twinge in his back.
"Technically it wasn't a good race because the bends are a little right and I wanted to take care of my injury before the world championships."
Olympic champion Merritt marked his return to the track with a second place
in the 400m and insisted he is now clean.
The 25-year-old clocked 44.74 sec with Jamaica's Jermaine Gonzales claiming victory in 44.69 sec, a season best. Chris Brown of the Bahamas was third in
"I wanted to come out and get a race, knock off the cobwebs. I feel good physically and I now want to get ready for the world championships," said Merritt.
"I am clean. My mother and my team believed in me and they will keep believing in me. Now I will go home and work on a few things and get ready for the worlds.
"At the worlds, I will be a contender, I always thought that and with a time today of 44.7, I can't complain."
Olympic and world champion Merritt tested positive for the anabolic steroid DHEA in three tests between October 2009 and January 2010.
Last October an American Arbitration Association (AAA) panel declared that his ban would end on July 27, less than the usual 24-month ban, thereby making Merritt eligible to compete prior to the world championships.
The arbitrators stated they believed his positive test stemmed from an inadvertent action and was not intended to produce a competitive advantage.
Merritt, who was not able to take part in the US national championships, was named in the US team last month for the world championships.
South Africa's 800m world champion Caster Semenya endured a miserable night on Friday, finishing eighth in her event in a time of 2min 01.28sec, with Jamaica's Kenia Sinclair claiming victory in 1min 58.21sec.
The 20-year-old Semenya, who clocked a personal best of 1:55.45 in storming to victory at the 2009 Berlin worlds but was then cast into limbo for almost a year because of allegations over her true gender, admitted she had been off colour.
"It was one of those days. I am quite happy with my performance even if I didn't run the race that I wanted to. I expected to run faster. I felt a little heavy," said Semenya.
"But I keep going. I never quit. Next time I hope to do better."
Olympic 110m hurdles champion Dayron Robles pulled out of his eagerly-awaited head-to-head with this year's world leader, the American David Oliver.
Robles injured his ankle last week in Barcelona and with the world championships in mind, he preferred not to risk running in Stockholm.
The Cuban is the world record holder (12.87secs) while Oliver has produced the best time this season of 12.91secs.
Jason Richardson of the US took victory in 13.17sec with Oliver in second spot in 13.28sec.
Kenya's Vivian Cheruiyot, the women's world 5000m champion, clocked the best time of the season of 14 min 20.87sec.
Olympic champion Yelena Isinbayeva, who hurt her hand in training last week and pulled out of the Lucerne meeting, won the women's polevault with 4.76m.
The 29-year-old Russian golden girl has set 27 world records in her career, but Friday's effort was way below her best ever mark of 5.06m.