Howe, who was also named Championship manager of the year after the Cherries’ title-winning season, is the first manager from outside the top flight to take the overall award since Steve Coppell, then of Reading, won in 2006.
The award came as recognition of Howe leading Bournemouth to the title, and promotion to the Premier League, with limited resources compared to many of his club’s rivals.
In comments reported on Bournemouth’s website, Brendan Rodgers, who presented the award to Howe, said: “He’s done a fine job, a remarkable job, and done it with style and humility.”
Bournemouth secured the title on the final day of the season as they beat Charlton 3-0 while Watford were held to a draw by Sheffield Wednesday.
Mourinho took the top flight award after a league and Capital One Cup double but did not attend the ceremony in London to collect it as he was at Chelsea’s own club awards event.
The Portuguese had already been named Barclays Premier League Manager of the Season despite not once winning the monthly award throughout the season.
Despite the accolades coming his way, Mourinho was still complaining about a perceived lack of recognition for his side in his speech at Chelsea’s event.
Mourinho said: “I don’t think my players got the respect that they deserve after what they did from day one until the last day.
“And these are words that I really feel, serious words.”
The League One award went to Steve Cotterill after Bristol City’s title-winning season.
The only divisional award not to go to the boss of the title-winning side was the League Two gong, which went to Wycombe’s Gareth Ainsworth despite his side losing the play-off final to Southend on penalties.
Bradford City’s Phil Parkinson was named FA Cup manager of the year after his side beat Chelsea and Sunderland en route to the quarter-finals of the competition.