The decision was made by the collegiate sports organization's student-athlete reinstatement staff the day after Auburn had declared Newton ineligible because of a violation of NCAA amateurism rules.
The Tigers are 12-0 and ranked No. 2 in the nation. They play South Carolina Saturday for the SEC championship.
Schools are required to declare a player ineligible when an NCAA rules violation is uncovered and can then request reinstatement of the player.
The NCAA said Newton was reinstated with no conditions.
The NCAA said in a release its enforcement staff and Auburn officials agree Newton's father and an owner of a scouting service worked together to actively market Newton as a part of a pay-for-play scenario in return for Newton's commitment to attend college and play football.
Because of the circumstances, Auburn University has limited the access Newton's father has to the athletics program and Mississippi State has distanced itself from the scouting service owner.
"The conduct of Cam Newton's father and the involved individual is unacceptable and has no place in the SEC or in intercollegiate athletics," said Mike Slive, Southeastern Conference commissioner. "The actions taken by Auburn University and Mississippi State University make it clear this behavior will not be tolerated in the SEC."
Kevin Lennon, NCAA vice president for academic and membership affairs, said the organization does "not have sufficient evidence that Cam Newton or anyone from Auburn was aware of this activity, which led to his reinstatement."
Auburn Athletics Director Jay Jacobs said the school was pleased with the outcome.
Former Mississippi State players have alleged Newton's father Cecil sought $100,000 to $180,000 for his son to sign with that school last year.