The 35-year-old striker announced this week he will retire at the end of this season to take up a post at the Rotterdam club's youth academy.
Makaay fired his third goal 15 minutes from time and was substituted minutes later, leaving the pitch in tears as he was given an ovation by the crowd.
"I didn't feel nervous before the match, because I never have felt that through my career, but I had a special feeling for my last league match. When I was substituted I realised it ended," Makaay told reporters.
Makaay headed home an equaliser after 13 minutes from close range and made it 4-2 after 58 minutes.
Two minutes before he was replaced by 17-year-old youth international Luc Castaignos, Makaay added his third with a 20-metre lob over goalkeeper Henk Timmer.
Makaay started his professional career in 1993 at Vitesse Arnhem but had his biggest successes later on with Deportivo La Coruna, where he won the Primera Division and became European top scorer, and Bayern Munich where he won the double in 2005 and 2006.
Makaay won 43 caps in which he scored six goals and will play in the second leg in the Dutch Cup final against Ajax Amsterdam, who won the first leg 2-0, on Thursday.
