The Welsh singer had been due to recommence his live tour after being forced to pull out of five performances due to illness.
He had recovered from a bacterial infection and had been given the go-ahead from doctors to play a show at the horse-racing venue today.
However, a tweet from York Racecourse's official twitter account revealed that due to bad weather conditions put a stop to the scheduled show.
It comes after singer James Arthur was forced to axe his open-air show in Scarborough last night (Thursday), over fears of lightning strikes on stage.
Read: James Arthur cancels open air Scarborough show over 'thunder and lightning' in YorkshireThe tweet said: "York Racecourse apologises to customers after thunder and lightning storms forced the cancellation of the Tom Jones Concert at York racecourse on Friday evening.
The 78-year-old had previously apologised to fans after he was forced to cancel the earlier shows while recuperating from his illness, during which he had been in hospital.
He was unable to perform at three concerts in the UK and one in Germany last week, and at Finnish rock music festival Down By The Laituri on Wednesday.
Sir Tom had said he was "extremely sorry and disappointed" at being unable to take to the stage.
He said it was the worst feeling "having to let down everyone who was coming as well as everyone who is involved" in the concerts.