Breida left Sunday's game against the Chicago Bears after reaggravating the ankle sprain which has plagued him for most of the season while Pettis left with an MCL sprain. Neither returned to the game.
"I think Matt's had a very impressive season," Shanahan said of Breida. "He started out great filling in (after) losing McKinnon at the beginning of the year. Matt stepped in right away and played like a No. 1 back. I think he was up there for a while close to leading the league in rushing. He's got a ton of explosives. Had good yards per carry.
"He got hurt early on, and he's battled every week to get in there and play for us, and he's ended up hurting it every week also, so it's lingered all year. Just a credit to him to still be effective when he's been out there and to be able to help us throughout the year has been unbelievable.
"He has not been 100 percent for a while, and that has affected his production. It has made it harder for him to look the same way he looked at the beginning of the year, but it shows you the type of guy he is and that he can still take it to a whole other level the healthier he gets for next year."
Shanahan also provided some other injury updates. Tight end Garrett Celek is in the concussion protocol while wide receiver Marquise Goodwin (calf contusion) and cornerback K'Waun Williams (knee) will be re-evaluated on Wednesday.
The 49ers made Pettis a second-round draft pick out of Washington in April. He has 27 receptions for 467 yards with five touchdowns through 12 games and seven starts this season. Pettis leads all wide receivers in receiving yards and all 49ers players in touchdown receptions.
The 49ers signed Breida as an undrafted free agent out of Georgia Southern in 2017. He has 814 rushing yards on 153 carries (5.3 yards per carry) with three touchdowns and has added 27 receptions for 261 yards with two receiving touchdowns through 14 games and 13 starts this season.
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