Per head coach Kyle Shanahan, No. 85 is trending in the right direction after suffering a groin injury early last week but still was not ready to go on Wednesday.
"He's made a lot of progress," Shanahan said. "Hopefully, we'll have better luck this week."
The timetable for Brunskill's return is less clear with the fourth-year offensive lineman suffering a recent setback in his recovery from a hamstring injury sustained during the preseason.
"He's closer than he was last week," Shanahan said. "He'll be in later this week, but I'm not sure yet. It's not good right now."
View game photos from the San Francisco 49ers Week 1 matchup vs. the Chicago Bears at Soldier Field.
In addition to Kittle and Brunskill, left tackle Trent Williams sat out of Wednesday's practice but only as a veteran rest day. Linebacker Dre Greenlaw was limited in his participation due to an elbow injury.
Wednesday also brought with it a slew of roster changes that included the promotion of defensive lineman Kemoko Turay to the active roster and the placement of another defensive lineman, Jordan Willis, on the Injured Reserve list due to a knee injury. The 49ers also signed three players to the practice squad: WR Willie Snead IV, RB Marlon Mack and CB Kary Vincent Jr..