General manager Sandy Alderson said Wednesday that the left-hander was going on the 15-day DL with inflammation in his lower back.
Doctors are not recommending surgery.
Santana has had an up-and-down season in his return from shoulder surgery that kept him out more than a year. He threw the team's first no-hitter June 1 but is 3-7 with an 8.27 ERA since throwing a career-high 134 pitches in that game.
He is 6-9 with a 4.85 ERA in 21 starts overall.
The two-time AL Cy Young Award winner is in the fifth season of a $137.5 million, six-year contract.
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