The six-time Olympic champion said the injury means he is “unable to compete at 100%” as it restricts his movement.
It is the latest setback for Bolt, following his withdrawal last week from the 100m at the Jamaican national trials.
But the 28-year-old says he will defend his 100m and 200m titles at August’s World Championships in China.
Bolt has had a poor season, running a best time of 10.12 seconds over 100m and 20.13 secs for 200m, while his rivals Justin Gatlin and Tyson Gay have been in much better form.
American Gatlin became the fifth fastest man over 200m in history on Sunday, clocking 19.57 secs, and has also run the fastest 100m of the year at 9.74 secs, while Gay ran 9.87 secs at the US trials.
Bolt, the world-record holder at 100m and 200m, will receive treatment in Munich on a blocked sacroiliac joint in the pelvis before resuming full training.
“I’m disappointed not to be able to compete in Paris and Lausanne,” said Bolt. “I love running at these meetings but at the moment I am unable to compete at 100%. I look forward to getting back into full training as soon as possible.”
Bolt is an eight-time world champion and has won six Olympic gold medals in his career.