Duncan Laurence singing Arcade beat 25 other contestants in the grand final in Tel Aviv to win the glass microphone trophy on Saturday.
"Believe in your music, believe in your artistry," Laurence said after his victory.
This year's competition was more political than usual, held against the backdrop of a campaign by the Boycott, Divestment, Sanctions (BDS) movement that urged artists, fans and broadcasters to shun the event to protest against Israeli policies in the West Bank and Gaza.
But no singers or broadcasters pulled out, and only a small crowd of protesters turned up outside the Expo Tel Aviv venue.
However pop superstar Madonna sprang a surprise during her guest performance of two songs - her iconic 1989 hit Like A Prayer and a new number, Future, sung alongside the American rapper Quavo.
At the close of the second number, two backing dancers briefly appeared on stage wearing the Israeli and Palestinian flags on the back of their costumes.
The European Broadcasting Union, which co-produced the contest alongside Israel's national broadcaster, issued a statement immediately after her performance. "This element of the performance was not cleared with the EBU and the Host Broadcaster, KAN. The Eurovision Song Contest is a non-political event and Madonna had been made aware of this," it said.
The 60-year-old singer, who is a follower of the mystical form of Judaism called Kabbalah, had faced criticism for performing at the event.
She defended her decision, saying on Tuesday that she would always speak up to defend human rights, and that she hoped to see “a new path toward peace.”
Hatari, Iceland's entrant, drew boos from the audience when the band held up small Palestinian banners live on air during voting. The EBU said the political display "directly contradicts the contest rules."
Security was tight through the final, with thousands of extra police, undercover officers and private security guards deployed. Fans had to pass through metal detectors and multiple security checks as armed patrols looked on from elevated positions.
A police spokesman said guards were searching not just for weapons but also for “materials that could be used for disruptions by potential BDS activists, including the flags of terrorist groups or flags that could be used by BDS activists”.
Israel says the calls to boycott the competition are discriminatory and anti-Semitic, which the BDS movement denies.
With its victory, the Netherlands wins the right to host next year's competition.
