There had been reports this week that the University of Arkansas had made Miles a lucrative offer to change jobs, but Alleva said that would not be happening.
Details of the new deal will be announced later, Alleva said, but he indicated a contract extension would be put in place in addition to the raise in salary.
Miles is currently under contract through 2017 at an annual salary of $3.75.
LSU went 10-2 this season, one of those losses being a last-second affair against then-No. 1 Alabama.
Miles has a record of 85-20 in eight seasons with the Tigers, who won the national championship under his guidance in 2007.
"Les Miles is one of the premier coaches in the country and has LSU in contention for championships year in and year out," Joe Alleva said. "Only two coaches in the 119-year history of LSU football have coached as many years at this school and only one has won more games. Les Miles has made a commitment to LSU and LSU is solidifying its commitment to Les Miles."
Benedict Cumberbatch's dramatic reading of R. Kelly lyrics is just what you need
Beyonce flaunts bikini body, Blue Ivy in vacation pics