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 separate 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.
Premier League Team of the Year: David De Gea (Manchester United), Pablo Zabaleta (Manchester City), Jan Vertonghen (Tottenham), Rio Ferdinand (Manchester United), Leighton Baines (Everton), Michael Carrick (Manchester United), Juan Mata (Chelsea), Gareth Bale (Tottenham), Eden Hazard (Chelsea), Luis Suarez (Liverpool), Robin van Persie (Manchester United).
npower Championship Team of the Year: Kasper Schmeichel (Leicester), Kieran Trippier (Burnley), Wes Morgan (Leicester), Mark Hudson (Cardiff), Wayne Bridge (Brighton), Wilfried Zaha (Crystal Palace), Thomas Ince (Blackpool), Peter Whittingham (Cardiff), Yannick Bolasie (Crystal Palace), Glenn Murray (Crystal Palace), Matej Vydra (Watford).
npower League One Team of the Year: Wesley Foderingham (Swindon), Simon Francis (Bournemouth), Robert Jones (Doncaster), Harry Maguire (Sheffield United), Charlie Daniels (Bournemouth), Matthew Ritchie (Bournemouth), Luke Murphy (Crewe), Alan Judge (Notts County), David Cotterill (Doncaster), Patrick Madden (Yeovil), Leon Clarke (Coventry).
npower League Two Team of the Year: Stuart Nelson (Gillingham), Sean Clohessy (Southend), Adam Barrett (Gillingham), Ryan Cresswell (Southend), Joseph Martin (Gillingham), Jacques Maghoma (Burton), Marlon Pack (Cheltenham), Gary Jones (Bradford), Jennison Myrie-Williams (Port Vale), Tom Pope (Port Vale), Jamie Cureton (Exeter).
Source: PA