Anchoring Racers in his first outing of the season, Bolt was unable to reel in Tyquendo Tracey, who crossed the line first to win in a world-leading 38.23 seconds at the National Stadium.
Bolt, the multiple-time Olympic sprint champion, brought Racers home second in 38.29 seconds.
He received the baton behind Tracey and despite making up significant ground, just failed to overhaul his rival.
“You want to win every time you go on the track, but this was a good race and I am feeling OK,” Bolt told the Jamaica Observer newspaper afterward.
Tracey said with Bolt chasing him down, he knew it was important to relax.
“I told myself to just relax and run,” Tracey said.
“Last year I got the lead but tightened up and (Yohan) Blake caught me, and I told myself I was not going to let lightning strike twice.”
Bolt led a star-studded team into the final with Commonwealth Games 100m champion Kemar Bailey-Cole, Olympic 200m silver medallist Warren Weir and Mario Forsythe joining him for the one-lap event.