Chris Biderman of the Sacramento Bee described Samuel as looking "close to 100 percent" in those runs.
Added Biderman: "Looks like he was moving well."
"We're still hoping he can get back for Week 1," head coach Kyle Shanahan said on Tuesday. "... I don't expect him back this week. We're still hoping on Week 1, but not sure."
While the 49ers have been cautiously optimistic about Samuel's recovery timeframe, the receiver has repeatedly vowed to be ready for the team's opener on September 13 against the Arizona Cardinals.
"He had his most intense workout thus far with change-of-direction exercises, etc.," added Matt Barrows of The Athletic.
The 49ers made Samuel a second-round draft pick out of South Carolina last year, and he hauled in 57 regular-season catches for 802 yards with three receiving touchdowns as a rookie. Samuel showed off his versatility with 14 rushing attempts for 159 yards with three more scores.