The trio had been nominated for the award along with Brentford’s Thomas Frank and Crystal Palace’s Patrick Vieira.
However, Klopp has been honoured after guiding FA Cup and Carabao Cup winners Liverpool to the Champions League final. The club finished second behind Guardiola’s Manchester City in the Premier League at the weekend.
Klopp also won the League Managers’ Association Manager of the Year award, and said: “It's a great honour, and it was an insane season. It was not the best outcome for us, but we’re already over it. When you win a prize like this, you’re either a genius – or you have the best coaching staff in the world. I’m here with all of my coaching staff, they know how much I appreciate them.”
Newcastle finished 11th with 49 points following an extraordinary turnaround. The club was winless when Howe took charge in November.