Harris' agent, Andy Simms, tweeted Monday that Harris will re-sign with San Francisco after the team did not tender him a restricted free agent contract earlier this month.
Harris played 10 games for the 49ers last season. He ran for 138 yards on 38 carries and also caught eight passes for 115 yards.
Harris has also played with Jacksonville, Green Bay and Seattle since entering the NFL in 2011. He has 590 yards rushing in his career on 145 carries.
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