Johnson was waived on Monday and his roster spot was taken by wide receiver Tim Patrick, whom the 49ers claimed off of waivers from the Baltimore Ravens.
"Johnson, we're still trying to decide on that because there was some partial stuff in his hamstring so there's a couple ways to go about it which we haven't decided yet," 49ers head coach Kyle Shanahan said just hours before the receiver was waived.
Johnson was originally signed by the 49ers as an undrafted free agent on May 8. He played college football at Georgia Southern. During his five-year career with the Eagles, Johnson played in 44 games, started 35, and registered 92 receptions for 1,377 yards and six touchdowns.
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