On Sunday, Blackburn claimed a 3-1 victory over Brentford, but Birmingham City's win away at Bristol City meant that the North-West side were demoted to the third tier of English football.
Owner Venky's have come in for fierce criticism since their arrival at Ewood Park, but they have moved swiftly to announce that Mowbray will continue in his role in the dugout.
A statement read: "The owners of Blackburn Rovers wish to place on record their appreciation for the work of manager Tony Mowbray since his arrival at the club, during which time both the performances of the team and results have improved significantly. Going forward he will continue to have our full support.
"Despite the courageous performance by the players and the victory at Brentford yesterday, results elsewhere led to the relegation of the club from the Championship. This is indeed a very sad situation and we are deeply hurt by these events. We share the same feelings as our supporters.
"Notwithstanding this temporary setback, we are confident that the collective efforts of the team, under Tony's leadership, will enable the club to achieve promotion back to the Championship next season."
Mowbray won five and drew seven of his 15 matches in charge during the closing months of the season.