Speaking alongside Palestinian President Mahmoud Abbas, Trump offered his condolences and condemned the "wicked ideology" that led to the attack.
Walking on the red carpet from the plane that had just brought them from the first leg of their trip in Saudi Arabia, Trump reached for his wife Melania's hand, who seemed to deftly yet subtly tap it away in a possible spurn captured by cameras and shared widely on social media.
Meanwhile, Abbas and the PA have continued to be viewed increasingly unfavorably by Palestinians, both due to the PA's recent violent suppression of demonstrators protesting against Israeli forces, as well as the authority's "revolving door policy" that effectively funnels Palestinians from PA jails into Israeli prisons, as part of its "escalating security collaboration" with Israeli authorities.
Relying on one of his preferred insults, Trump said he would call the perpetrators "losers, because that's what they are".
He became the first sitting USA president to visit the site in the Israeli-annexed east of the city.
"And it's so interesting that our meeting took place on this very awful morning of death to innocent young people", he said, referencing the late Monday bombing outside of an Ariana Grande concert in Manchester, UK.
The U.S. president also pledged his support for renewed Israeli-Palestinian peace negotiations.
Hundreds of stone-throwing youths clashed with Israeli soldiers firing tear gas and rubber bullets.
Mr Trump spoke from Bethlehem in the West Bank, the morning after a blast that killed 22 people at an Ariana Grande concert.
The most high-profile moment of Trump's stay in Jerusalem was his visit to the Western Wall, one of the holiest sites in Judaism.
The West Bank, including East Jerusalem, has been occupied by Israel for 50 years.
Trump was set to leave later Tuesday afternoon on his way to the Vatican. "Iran must never be allowed to possess a nuclear weapon", Trump said, standing beside Israeli President Reuven Rivlin.
In return, Mr Netanyahu extolled the USA president's leadership.
Oren Hazan, who has become known in the region for his inappropriate antics, pulled out his cell phone as President Trump walked past him on Monday before snapping a photo. Trump's two-day visit came immediately before the Israeli holiday of Jerusalem Day, which this year marks the 50th anniversary of Israel's reunification of the holy city during the Six-Day War.
On Wednesday he will continue to Brussels to see North Atlantic Treaty Organisation leaders.