With the new agreement, Pinkel's guaranteed salary will increase $300,000 to $3.1 million.
Last season, the Tigers went 12-2 and won the Southeastern Conference Eastern Division title, reaching the SEC Championship Game in the program's second year in the league.
Mizzou also defeated Oklahoma State, 41-31, in the Cotton Bowl, finishing with a final ranking of fifth - the second-highest finish to a season by any Tiger team.
"I'm very honored and proud to be the coach at Mizzou, and I appreciate the opportunity," said Pinkel. "We will work very hard to continue to build our program and to graduate our players. It's important for our program to keep moving forward and build on a solid foundation. I'm pleased that my assistant coaches continue to get recognized for the work they do. We are fortunate to have a great staff at Mizzou."
The Cotton Bowl victory was also historic, as it made Pinkel the winningest coach in Mizzou history. With a record of 102-63 in 13 seasons, Pinkel passed legendary coach Don Faurot, who went 101-79-10 in 19 seasons.
"It is important for us to be able to recognize what Gary and his staff have achieved for the University of Missouri," said Director of Athletics Mike Alden. "We're very grateful to the Board of Curators and University leadership for their support of our program, which is among the best in the nation both academically and competitively."
Since 2007, Mizzou is the only program in the country to rank in the top-10 nationally in wins, while also ranking in the top-five in both Academic Progress Rate.
Mizzou Athletics is currently in the midst of a $200 million facilities improvement process - largely related to football - as a sign of its commitment to competing in the SEC and on the national level.
Also part of the deal is in increase in the assistant coaching staff salary pool from $2.66 million to $3.2 million.