The ATP number four was top seed at the German event which marks the start of the grass season transition prior to Wimbledon, which begins on July 1st.
The German lost the Paris final after over four hours on court against Carlos Alcaraz on Sunday.
"I have played a lot of tennis in the last few weeks and reached the final in Paris, where I played five tough sets," Zverev said in a statement.
"I feel that my body is not ready to go from clay to grass now."
Zverev last competed in Stuttgart in 2019, losing his opening match to Dustin Brown.
Zverev was replaced in the Stuttgart draw by French veteran Richard Gasquet, who will play Brandon Nakashima after the American beat compatriot Christopher Eubanks 7-6(4), 6-4 on Tuesday.