The PFA came under fire last week for their refusal withdraw Suarez from its Player of the Year shortlist after he bit Branislav Ivanovic during Liverpool's game against the Blues at Anfield.
In a room full of fellow professionals and other guests at the Grosvenor Hotel in Mayfair, central London, where the awards were handed out, the controversial Uruguayan's name was booed on two occasions.
The first time came when he was named in the team of the year, and secondly when his name was read out on the short list for Player of the Year, in which he finished second behind Gareth Bale.
Suarez, who has scored 23 goals in the league this year, received an eight-match ban for racially abusing Manchester United defender Patrice Evra last season.
Suarez was the only Liverpool player named in the team of the year.
Premier League top scorer Robin van Persie was one of four Manchester United players to be included in the XI.
Van Persie, who moved to Old Trafford from Arsenal last summer, has scored 25 goals so far this term to help United win their 20th Barclays Premier League title.
He was joined in the Team of the Year, which is voted for by the players, by team-mates David De Gea, Rio Ferdinand and Michael Carrick.
Deposed champions Manchester City only had one member in the team - Argentinian right-back Pablo Zabaleta.
Gareth Bale, who also won the Player and Young Player of the Year awards, earned a place in the team, while his Tottenham team-mate Jan Vertonghen was named in central defence.
Chelsea duo Juan Mata and Eden Hazard were also included, as was Everton left-back Leighton Baines.
Wilfried Zaha, who will joined the Premier League champions earlier this year and was immediately loaned back to Crystal Palace, was named in the npower Championship team of the year alongside Eagles team-mates Glenn Murray and Yannick Bolasie.
There was no place in the starting XI for Blackburn's Jordan Rhodes, with Watford hitman Matej Vydra preferred up front.
Peter Whittingham and Mark Hudson were the two representatives from champions Cardiff while Blackpool's Tom Ince was also included.
Newly-promoted Doncaster had two players - David Cotterill and Rob Jones - named in the npower League One team of the year and there was also a place in the team for top scorer Patrick Madden, who has scored 23 goals this season for Yeovil.
Gillingham, who will be playing in League One next season, had three players included in the League Two team of the year - Stuart Nelson, Adam Barrett and Joseph Martin.