Coach Norv Turner refused to give an injury update on the trio. Since the Chargers host Denver on Monday night, they don't have to issue their first injury report of the week until Thursday.
Turner says he's confident the three will be able to play.
Gaither strained his groin late in a 31-24 loss at New Orleans and gave up a sack during which Philip Rivers lost a fumble to the Saints.
It wasn't clear why Mathews and Clary were held out.
Cornerback Shareece Wright practiced for the first time since spraining an ankle in the season opener.