The PFA received criticism last week for refusing to remove the Uruguayan from their Player of the Year shortlist, after the 26-year-old was handed a 10-match ban for biting Branislav Ivanovic the previous weekend.
Suarez, who has netted 23 goals for the Reds this season, had his name booed on two separate occasions during the ceremony.
The first was when he was listed in the PFA Team of the Year, with the second incident arriving when he was named as runners-up to Gareth Bale for the Player of the Year award.
The controversial forward received an eight-match ban last season for racially abusing Patrice Evra, while he has also come under fire for allegedly going to ground too easily.
Suarez was the only Liverpool player to be named in the PFA Team of the Year.