The reigning world champion, 31, had dropped to ninth place following the shot put, the third event of the opening day of the competition.
Her coach, Aston Moore, said the decision had been taken due to a "small niggle in her right leg".
Moore added: "We don't want to risk losing any time from training which could be the result if she was to carry on competing with it for another day."
Twelve months after winning her second world title, Johnson-Thompson will bid for a first Olympic medal in Paris this summer, where two-time champion Nafissatou Thiam will represent the Briton's main obstacle to gold.
It is for that anticipated showdown that both athletes are aiming to be at their peak, and ultimately the reason why Johnson-Thompson has chosen not to continue in Italy.
She ended the morning session fourth overall, running the 100m hurdles in 13.66 seconds before clearing 1.83m in the high jump.
And her deficit to Thiam, who led the standings after a best in the high jump of 1.95m, increased to 318 points as a throw of 12.44m in the shot put left her ninth on Friday evening.
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