The pact includes a $50,000 annual raise.
Stewart is in his first season as head coach of the 25th-ranked Mountaineers following the unexpected departure of Rich Rodriguez to Michigan at the end of the 2007 regular season.
He took the WVU post on an interim basis, and was named head coach full time on Jan. 3 when the Mountaineers trounced Oklahoma 48-28 at the Fiesta Bowl.
"Coach Stewart has worked tirelessly to assemble a staff, recruit an outstanding class of student-athletes and prepare for the season," Athletic Director Ed Pastilong said on the school's Web site. "With most terms and conditions agreed to in June, it was a matter of both parties reviewing the document before signing the agreement. I look forward to Coach Stewart's continued leadership."