The 50-year-old who arrived at the Etihad in 2016 from Bayern Munich – reclaimed the Premier League title with City, won the League Cup for a fourth time and faces Chelsea in the Champions League final on Saturday.
The five other managers who received the most votes were Marcelo Bielsa, Daniel Farke, Emma Hayes, David Moyes and Brendan Rodgers.
Guardiola said: ‘I am delighted to win the LMA manager of the year award for the second time.
‘It is, for me, such a special trophy to win because it is voted for by my fellow managers. An award like this is only possible though if a manager is surrounded by top professionals.
‘My players have been fantastic – their dedication and professionalism never wavered, even in a season that has been the most challenging we have ever faced.
‘And my staff are also deserving of the highest praise. I am so lucky to have a team of people who give everything they have every single day to make sure Manchester City are the best we can be.
This award is dedicated to and shared with them.’
Guardiola won a third Premier League crown with City after they finished 12 points ahead of Manchester United.
Norwich manager Farke, Hull boss Grant McCann and Cheltenham chief Michael Duff won the awards for their respective divisions.
Chelsea’s Hayes won the Barclays FA Women’s Super League manager of the year while Rangers boss Steven Gerrard was presented with the LMA special achievement award after going unbeaten to win the Scottish Premiership.
LMA chairman Howard Wilkinson said: ‘Many congratulations to Pep on winning his second LMA manager of the year award, following a season which epitomises his career to date.
‘He never gives up, he is humble in victory and defeat and he is always respectful of his opponents, who in turn have shown him the ultimate respect in voting for him to win this award.’
Sir Alex Ferguson, an LMA committee member, also praised Guardiola: ‘As well as being a truly gifted manager and leader, you always display admirable humility and composure and I am sure your family must be very proud of you.’
The former Barcelona boss has transformed City into a true force during his five years in the Premier League – winning 10 trophies and guiding them to the brink of European glory.
He was able to get his hands on yet another Premier League title on Sunday after his side thrashed Everton 5-0, and during the celebrations he said this particular triumph felt more special because of the problems the pandemic had posed.
‘We are lucky to have people here when we lift the trophy – it is not a full stadium but there is enough noise for us to enjoy it with them,’ he said.
‘It feels completely different, it’s much better. Every title is nice. This one is different because of the pandemic and the problems that every one of us have had. That’s what makes it special.’