Financial terms of Thomas' deal weren't disclosed.
"Tra is a talented player with a wealth of starting experience," Chargers general manager A.J. Smith said in a statement released by the team. "We have held him in high regard for many years. He will be added to the mix as we move forward in preparation for the upcoming season."
McNeill, outside linebacker Shawne Merriman and wide receiver Vincent Jackson are so unhappy about being tendered one-year contracts as restricted free agents that they have skipped offseason workouts, including mandatory minicamps. Their holdouts could extend into the regular season.
Tuesday is the deadline for teams to withdraw original qualifying offers to unsigned restricted free agents and still retain exclusive negotiating rights by substituting a tender of 110 percent of the previous year's salary. Merriman was tendered at $3.269 million, Jackson at $3.268 million and McNeill at $3.168 million.
The San Diego Union-Tribune reported Tuesday that the Chargers sent Jackson and McNeill letters warning them their salaries will be cut deeply if they don't sign their tenders by the deadline. Jackson's salary would be reduced to $583,000, McNeill's to $600,000.
Wide receiver Malcom Floyd ended his holdout Monday by signing his $3.168 million tender.
Thomas, 35, was a first-round draft pick of the Philadelphia Eagles in 1998, and he went to the Pro Bowl after the 2001, '02 and '04 seasons. He played in five NFC Championship Games and one Super Bowl with the Eagles.
Thomas signed with the Jacksonville Jaguars last year and played in eight games, starting one.
The Associated Press contributed to this report.