San Francisco announced the move during its off day Monday before Week 1 preparation begins in earnest ahead of Sunday's season opener against Green Bay.
Harper was a fourth-round draft pick by the NFC West rival Seattle Seahawks, who released him Saturday.
Also Monday, the 49ers traded linebacker Cam Johnson to the Colts. The team added seven players to its practice squad: tackle Carter Bykowski, running back Jewel Hampton, wideout Chuck Jacobs, cornerback Darryl Morris, guard Patrick Omameh, nose tackle Mike Purcell and safety Michael Thomas.
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