The British rocker performed late Thursday in front of a screaming crowd of nearly 50,000 fans at a Tel Aviv stadium.
John, who wore blue-tinted sunglasses, told the audience those cancellations "ain't gonna stop me from playing here, baby."
Recent cancellations by the Pixies and Elvis Costello, who cited Israeli government policies, have added to Israel's growing sense of isolation.
John swiped at those artists, saying, "We do not cherry-pick our consciences," before hitting the opening chords of his 1972 hit "Crocodile Rock."