However, she also set Washington on course for a possible disagreement with Benyamin Netanyahu, the Israeli prime minister-designate, who has spoken of Palestinian self-government but avoided conceding a two-state solution.
Clinton, who arrived in Jerusalem after attending a donors' conference aimed at addressing the needs of the Gaza Strip after Israel's 22-day assault, said that Barack Obama, the US president, believed a separate Palestinian state was fundamental for achieving peace.
"During the conference, I emphasised President Obama's and my commitment to working to achieve a two-state solution to the conflict between Israel and the Palestinians and our support for the Palestinian Authority," she said.
Though Obama has said that an Arab-Israeli peace deal will be a priority during his presidency, talks between Israeli officials and the Palestinians have stalled over violence, settlement-building and disputes over other core issues such as the future of Jerusalem and Palestinian refugees.
The West Bank-based Palestinian Authority suspended the negotiations after Israel launched it devastating offensive on Gaza, with a stated aim of ending Palestinian rocket fire into the south of the country.
Clinton, who met Netanyahu later on Tuesday, defended Israel's right to respond to rocket and mortar attacks.
"The continuing rocket attacks against Israel must cease," she said.
"There is no doubt that any nation, including Israel, cannot stand idly by while its territory and people are subjected to rocket attacks."
Al Jazeera's Jacky Rowland, reporting from Jerusalem, said the the US and Israel were "testing the waters" to see how they will move forward on the Israel-Palestine issue.
"The Israelis [are] getting a sense of whether the new [US] administration is going to be substantially different in substance as well as in style and the Americans [are] really conveying to the Israelis that they hope to have a different spirit in their approach to the Middle East," she said.
"... It will be really a case of waiting until the next visit when there is a new government in Israel to see whether the US is going to be more forthright in pushing that government to try to achieve some progress in the negotiations with the Palestinians, a process that really withered and faded under the previous US administrations."
The US continues to take a tough line against Hamas, which effectively controls the Gaza Strip.
In Egypt on Monday, Clinton pledged $900m to rebuild Gaza but maintained the money would be channelled through the Palestinian Authority rather than being paid to Hamas.
At another press conference later on Tuesday, Clinton said that two US officials would be sent to Syria for preliminary talks on improving relations between the two countries.
"We're going to dispatch a representative of the state department, a representative of the White House, to explore with Syria some of these bilateral issues," she said, alongside Tzipi Livni, Israel's foreign minister.
"[But] we have no way to predict what the future with our relations concerning Syria might be."
The two US officials are said to be Jeffrey Feltman, acting assistant secretary of state for Near Eastern affairs, and Dan Shapiro of the White House's National Security Council.
Relations between the US and Syria had been strained with George Bush, the former US president, even including Damascus among his "axis of evil" countries.