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.