The awards ceremony, held at the Grosvenor Hotel in Mayfair, was attended by fellow professionals and guests who jeered the star following his recent behavior.
The controversial Uruguayan's name was first booed upon the announcement that he had been selected in the team of the year, before being heckled a second time when his name was read out on the shortlist for Player of the Year.
Gareth Bale was declared the winner with Suarez finishing in second place and the Reds striker was the only member of the Liverpool squad to feature in the team of the year.
Suarez has scored 23 goals for the Reds in the league this campaign but has seen his season draw to a premature end following a ten-match ban for biting Chelsea's Branislav Ivanovic.
It follows a previous eight-match ban received last season when Suarez racially abused Manchester United left back Patrice Evra.
The PFA had been under pressure to remove Suarez from the awards shortlists following his actions at Anfield on April 21, but the organization refused and opted to keep the 26-year-old in contention.
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