Despite his side faltering in the final stages of a thrilling title race which had Manchester City winning the Premier League by two points, it was Rodgers who received the majority vote of the 92 league managers.
It has been the attacking style of Liverpool that has won over many neutrals in a sizzling campaign in the top flight and on picking up the award, Rodgers, referring to the City celebration in Manchester, joked: "I was hoping to be on the open-top bus tonight."
LMA chairman, Howard Wilkinson, said: "There can be no greater tribute to a manager and his work than a tribute awarded by his match day foes and peers. We applaud Brendan Rodgers as he receives that most valuable award.
"Liverpool's performances and results this season have provoked memories of some of those momentous years in the past when they had to contend with those two Uniteds - the first from Leeds, the second from Manchester.
"For Liverpool and Brendan, I'm sure we all hope this season marks the beginning of a new voyage and a new era."
Pulis can reflect proudly on a magnificent six months at Palace after looking doomed in November and were stuck in the drop zone when the 56-year-old replaced Ian Holloway.
Having accumulated four points from their opening 11 games to sit six points from safety, the Welshman took the reins and steered the Eagles up to 11th place and was rewarded for his efforts with the division's award.
It was the first time in five attempts that the London side had survived a season in the Premier League without being relegated.
On receiving the award, Pulis said: "We finished sixth in the Championship last season and 11th in the Premier League this season. That's a 15 place jump!
"But it's not just about me. It's about Steve Parish (chairman) and three other directors, the supporters and the players."
The Championship Manager of the Year award went to Nigel Pearson for steering Leicester City up to the Premier League.
League 1 joint Managers of the Year were Wolverhampton Wanderers boss Kenny Jackett and Leyton Orient's Russell Slade.
The League Two Manager of the Year prize went to Scunthorpe United's Ross Wilcox who was also presented with a Special Merit Award by Sir Alex Ferguson for his 28 game unbeaten run.
FA Cup Manager of the Year was Nigel Clough following Sheffield United's run to the semi-finals.