Tight end Kittle and linebacker Warner missed practice for the second successive day. Kittle is dealing with a rib injury while Warner suffered an ankle injury against New England that forced him to miss the entire second half.
Kittle and Warner were seen doing conditioning work in pads during the portion of practice open to the media.
Asked by KNBR about the playing status of Kittle and Warner, head coach Kyle Shanahan said on Thursday: "Still not sure yet. They haven't been good enough to go today, which is never fun.
"They're two guys who, if they don't practice, can definitely play on Sunday. So hopefully they'll get there."
In other words, Kittle and Warner will be given every chance to play, and their absences from practice could be related to the 49ers wanting to manage their workload with a short week coming in Week 6 against the Seattle Seahawks.
Still, it is a concern that neither was able to take part in the penultimate practice of the week, and the 49ers have other worries away from that pair.
49ers injury report
49ers
The biggest issue outside of Kittle and Warner is related to defensive lineman Yetur Gross-Matos, who played a key role last week with his ability to rush the pass off the edge and from the interior in the wake of defensive tackle Javon Hargrave's season-ending injury .
Gross-Matos missed practice for the second straight day and, if his knee injury keeps him out, that will rob the 49ers of some much-needed flexibility up front. Should he fail to recover in time, look for Sam Okuayinonu's snap count to increase following another strong outing in Week 4.
Linebacker Demetrius Flannigan-Fowles, who had been starting at SAM linebacker, also appears set to miss out with a calf issue. Flannigan-Fowles was limited on Wednesday but looks to have suffered a setback after missing Thursday's practice.
Better news at linebacker came as Dee Winters returned to practice. Winters' ankle problem kept him out of Wednesday's session, but he will likely be in line to start if one of Warner or Flannigan-Fowles can't go.
Meanwhile, cornerback Isaac Yiadom was a new addition to the injury report with a thigh problem, which meant he was limited. The veteran has endured an at best inconsistent start to his 49ers career as the third cornerback and his injury could see rookie Renardo Green take Yiadom's spot.
Elsewhere in the secondary, Talanoa Hufanga seems primed to make his return after missing the Patriots game. The 2022 first-team All-Pro was again limited with ankle injury he suffered in last Thursday's practice.
The situation is looking bright on the interior defensive line, with Kevin Givens (tricep) and Jordan Elliott (knee) each practicing for a second straight day and Kalia Davis (knee) again practicing in full.
San Francisco opened Davis' practice window this week after he underwent surgery following the first preseason game, leading to him going on injured reserve. The 2022 sixth-round pick looks on track to be activated back to the 53-man roster and will likely see significant snaps if the 49ers make that move.
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