Clinton made the comments in a joint news conference with Mikheil Saakashvili, the Georgian president, during the final stop of a regional tour aimed at promoting democracy and strengthening US ties in the region.
Clinton also called on Saakashvili to strengthen the country's democratic institutions.
She urged further reforms in Georgia, saying a vibrant democracy and economy were vital for Georgia to regain control of the breakaway regions.
"The more vibrant, effective a democracy and economy Georgia becomes, a greater contrast there will be between South Ossetia and Abkhazia and the rest of Georgia," Clinton said.
US officials have repeatedly voiced support for Georgia's territorial integrity since the country's 2008 war with Russia, which saw Russian forces pour into the country to repel a Georgian military assault on Moscow-backed South Ossetia.
Saakashvili said he was encouraged that the US was continuing to stand by Georgia despite a "reset" in Washington's relations with Russia.
"With regard to reset, it's a clear-cut issue that questions were asked. There is no secret about it, of course some people were worried what it might mean," he said.
"We see it's done exactly the right way, it's a value-based policy and that's why we all love America ... ultimately if reset leads to a more modernised Russia that's only good for all of us."
After the war, Russia recognised South Ossetia and Abkhazia as independent states, a move that has been followed by only a handful of states.
Russia has since established permanent military bases and deployed hundreds of troops and border guards in the regions.
Clinton said Washington was concerned about the construction of the military bases and would not accept Russian spheres of influence.
Ex-Soviet bloc tour
Clinton began her ex-Soviet bloc tour on Thursday in Ukraine, and went on to visit Poland, Azerbaijan and Armenia.
Her visit to Azerbaijan on Sunday was seen as a fence-mending mission to ease a strained relationship with the country, which had been bereft of a US ambassador for more than a year.
She appealed to Armenia and Azerbaijan for a peaceful resolution of a long-running territorial dispute between the neighbouring ex-Soviet states, telling leaders of both countries to act quickly towards settling the dispute.
The Nagorno-Karabakh dispute has caused problems in the diplomatic relations of several countries since a 1994 ceasefire ended a three-year war that claimed up to 30,000 lives.