She met the President, Sheikh Mohamed, to pay her respects.
She also greeted Sheikh Abdullah bin Zayed, Minister of Foreign Affairs and International Co-operation.
Accompanying her were John Kerry, special presidential envoy for climate, Philip Gordon, Miss Harris's national security adviser, CIA director Bill Burns, and White House Middle East co-ordinator Brett McGurk.
Ms Harris was welcomed to the capital by Sheikh Khaled bin Mohamed bin Zayed, Abu Dhabi Executive Council member and chairman of the Abu Dhabi Executive Office, and Sheikh Tahnoun bin Zayed, national security adviser.
She was also greeted by US Secretary of State Antony Blinken, US Secretary of Defence Lloyd Austin, Barbara Leaf, special assistant to the president and senior director for the Middle East and North Africa, National Security Council, and Sean Murphy, Chargé d’Affaires, US Embassy Abu Dhabi.
Ms Harris paid tribute to Sheikh Khalifa on Friday, praising his efforts to bolster Emirati-US ties.
“Under his leadership, the strong partnership between the United States and the UAE has enhanced the security and prosperity of the American and Emirati people, and we are grateful for our work together across multiple administrations,” she said.
“The legacy of this partnership can be found in the deep bonds between our countries, which our administration will continue to strengthen.”
Mr Blinken wrote on Twitter: “Vice President Harris, Secretary of Defence Lloyd Austin and I offered our condolences to the leaders and people of the UAE today for the passing of HH Sheikh Khalifa bin Zayed. We mourn his passing and honour his legacy.”
She had been a rising star in Democratic politics for much of the past two decades, serving as San Francisco's district attorney and California's attorney general before becoming a US senator.
After she ended her own 2020 Democratic presidential campaign, Mr Biden selected her as his running mate.
On Friday, the US president said he was “deeply saddened” to learn of the death of Sheikh Khalifa, who had served as president since 2004.
“Sheikh Khalifa was a true partner and friend of the United States throughout his decades-long tenure as President of the United Arab Emirates and Ruler of Abu Dhabi, and in his earlier role as Crown Prince of Abu Dhabi,” Mr Biden said.
Mr Biden congratulated Sheikh Mohamed on his election as president.
“Sheikh Mohamed, whom I met with several times as vice president when he was the Crown Prince of Abu Dhabi, has long been at the forefront of building this partnership,” he said.
“I look forward to working with Sheikh Mohamed to build from this extraordinary foundation to further strengthen the bonds between our countries and peoples.”