Spaniard Guardiola led City to the Premier League title with a record 100 points, scoring 106 goals and dropping just 14 points all season.
Guardiola collected his accolade at the LMA Awards dinner in London on Tuesday night, having 24 hours earlier enjoyed celebrating City's triumph with an open-top bus parade around Manchester.
City also secured a record number of wins for a single campaign with 32.
Liverpool's Jurgen Klopp, Burnley's Sean Dyche, Wolves boss Nuno Espirito Santos, Cardiff manager Neil Warnock and Accrington Stanley's John Coleman were also on the shortlist.
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Boston had no such problem with scoring distribution - with all five starters plus Marcus Smart scoring in double-figures. Still, he wasn't almost as impactful in the second half as the Celtics pulled away for a 107-94 win.
The series follows the season of the Premier League champions and offers interviews with players and coaches, showing the week-to-week lives of those involved over the course of the season.
Nobody came remotely close to challenging the rampant brilliance of City this season but it was United, despite all their problems under Mourinho, who showed this term that they are the most likely to give them a run for their money next time around. They had an fantastic season.
'I am at a fantastic club - it is a family. "I don't know what is going to happen in the future but we will always remember together that we did it here in England".
"Everybody wants to be here".
That heavy investment paid off with City winning the Premier League and League Cup, but Guardiola said fans should not expect similar spending. "Ultimately, at the end of next season if Pep wins another league that will be a big problem over a three-year period".