Other artists such as The Pixies and Elvis Costello scrapped gigs over the country's raid on a Gaza aid ship, which killed nine people.
Costello cancelled two planned gigs in Tel Aviv on June 30th and July 1st, saying it was "a matter of instinct and conscience".
John, 63, resisted calls by pro-Palestinian activists to cancel the concert, telling almost 50,000 fans in Tel Aviv: "Ain't gonna stop me from coming here, baby."
He added: "Musicians spread love and peace, and bring people together. That's what we do. We don't cherry-pick our conscience."
The Tel Aviv gig follows another controversial concert by the star, as he recently earned $1 million for playing at the wedding of American gay rights opponent Rush Limbaugh.
John has not commented on why he played the gig, but his civil partner David Furnish said he wanted to "build bridges" with those whose opinions he disagrees with.
Source: Pink News
Not particularly surprising, considering the man played at Rush Limbaugh's wedding, of all people. I already disliked him