Even US' close allies including UK, France, Germany and Saudi Arabia along with other GCC countries had condemned the move.
"Jerusalem is key to Muslims and Christians as it is to Jews", he added.
Pence is set to meet with Jordan's King Abdullah II on Sunday and visit with USA troops in the region.
Before traveling to Israel, Pence was in Jordan where King Abdullah expressed concern about the Jerusalem decision and urged the United States to "rebuild trust and confidence" in the search for a two-state solution. "This has to come through direct negotiations", said Mogherini.
Meeting at the presidential palace in Cairo, the two leaders discussed ways to combat the growing terror threat in the region.
Netanyahu again lauded the Jerusalem decision. "Today, we have a major challenge to overcome, especially with some of the rising frustrations".
Jerusalem is claimed as capital by both Palestinians and Israelis, with the US and other countries previously housing their embassies in neutral Tel Aviv instead to avoid stoking tensions.
The king said on Sunday he hoped Pence's visit, the second leg of his regional visit, would "rebuild trust and confidence" after the United States decision last month to name Jerusalem as Israel's capital. No country in the world now has an embassy in the city.
He reiterated his long-standing demand that the Palestinians recognise "the Jewish people's right to a nation state in its land, a nation state of its own here in the land of Israel".
Palestinians and Arab Israelis boycotted Pence's visit after Trump broke with decades of USA policy by announcing the embassy move. President Mahmoud Abbas is now in Brussels for meetings with European Union officials in which he will call on the bloc to recognise a Palestinian state, according to the AFP news agency.
Nabil Abu Rdeneh, an Abbas adviser, reiterated that 'the USA is no longer acceptable as a mediator'.
"By finally recognizing Jerusalem as Israel's capital, the United States has chosen fact over fiction - and fact is the only true foundation for a just and lasting peace".
"Anyone who truly wants to fulfil those goals knows there is no substitute to the United States' leadership", said Netanyahu, who is due to hold talks with Pence on Monday.