Pence's comments, though routine, had significance for Indonesian President Joko "Jokowi" Widodo, who a day earlier suffered a serious political setback when a political ally was defeated by Islamic conservatives in the election for Jakarta governor.
The divisive campaign undermined the image of Indonesia abroad as a generally tolerant Muslim nation.
Indonesia is the latest stop on an Asian tour by Pence that aims to reaffirm traditional US alliances at a time when Donald Trump's presidency has raised questions about the strength of the US commitment to the region.
The vice president praised Indonesia for its moderate form of Islam and said the two countries would continue to cooperate on combating terrorism.
"As the second- and third-largest democracies in the world, our two countries share many common values including freedom, the rule of law, human rights and religious diversity," Pence said.
"The United States is proud to partner with Indonesia. It promotes and protects these values."
The vice president added: "Indonesia's tradition of moderate Islam frankly is an inspiration to the world and we commend you and your people. In your nation as in mine, religion unifies, it doesn't divide."
Trump assailed the Trans-Pacific Partnership trade deal during his 2016 campaign and announced shortly after his inauguration that the US would withdraw from the Pacific Rim- based TPP, which now includes 11 countries from Chile to New Zealand.
Pence has sought to reassure allies in the region that the US is still committed to trade and economic ties despite Trump's decision on TPP.
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