The NFL did not release details of the substance abuse violations. Smith, the leading receiver in franchise history, issued an apology through the team.
"I would like to apologize to my families, friends, the Jaguars organization and fans," Smith said. "I am sincerely sorry that I have concealed this from everyone and let them down."
Smith, 34, will be allowed to play the remainder of the pre-season but must sit out the first four regular-season games. He will not be eligible to rejoin the team until Sept. 29.
Smith, who started his career with Dallas in 1992, has had at least 1,000 yards receiving in seven straight seasons. Last season, he had 80 catches for 1,027 yards and seven touchdowns.