Missouri became the first school to be fined under the SEC's revised policy after fans rushed the field in Columbia following Saturday's 30-27 walk-off win over Kansas State.
Because it was Missouri's first offense, the school will pay $100,000.
The money will go to the SEC Post-Graduate Scholarship Fund.
The conference, during its annual spring meetings, voted to increase fines for violating the field access policy. A school's second offense will result in a $250,000 fine. A $500,000 fine will be handed out for third and subsequent offenses.
According to the policy, "institutions shall limit access to competition areas to participating student-athletes, coaches, officials, support personnel and properly credentialed or authorized individuals at all times. For the safety of participants and spectators alike, at no time before, during or after a contest may spectators enter the competition area."
Missouri beat then-No. 15 Kansas State on Harrison Mevis' 61-yard field goal that split the uprights with no time left.
Mevis' kick set the record for the longest field goal in SEC history. The previous record was 60 yards, done three times, most recently in 1984 by Georgia's Kevin Butler and Florida's Chris Perkins.
The Tigers, who improved to 3-0, will host Memphis on Saturday.