Perry died April 25 at 84, and Johnson, 81, died Friday. Their families agreed to submit their brains for the BU study into head injuries and the neurodegenerative disease chronic traumatic encephalopathy (CTE).
Perry's widow, Donna, told the newspaper she had suspicions her husband suffered from CTE.
"You're starting to see them paying attention to it and trying to protect (players)", she said. "The guys will always play sports -- they're part of our lives -- but there should be some sort of protection. When Joe was playing, they'd give them smelling salts and put them back in. Now the equipment is better, and they're looking into ways to protect them. We have to look at what this is doing to our children."
Kathy Moppin, Johnson's daughter, said her father had been confined to a wheelchair for several years and was unable to speak or swallow for the past year.
After one year in the Canadian Football League, Johnson entered the NFL in 1954 as a member of the 49ers' vaunted "Million Dollar Backfield," which also included running backs Perry and Hugh McElhenny and quarterback Y.A. Tittle. The group remains the only full-house backfield to have all four of its members enshrined in the Pro Football Hall of Fame.
Johnson spent the 1966 season with the AFL's Oilers before retiring. At that time, he trailed only Jim Brown, Jim Taylor and Perry on the NFL's career rushing yards list. Johnson now ranks 55th.
Johnson also made 186 receptions for 1,478 yards, and he scored 55 touchdowns. He made the Pro Bowl four times, in 1955, 1963, 1964 and 1965.
Perry was the first player with back-to-back 1,000-yard rushing seasons and nicknamed "The Jet" for his sensational speed.
Perry finished with 9,723 yards rushing on 1,929 carries with 71 touchdowns in 181 career games. He also had 2,021 yards receiving on 260 catches for 12 touchdowns. He broke the NFL record for most career yards rushing, a total that was later topped by Jim Brown.
The Associated Press contributed to this report.