The Topol RS-12M missile was fired from the Kapustin Yar test range near the Caspian Sea, hitting a target in the Sary Shagan range in Kazakhstan.
The US received prior notification in accordance with the nuclear arms treaty that exists between the countries. Mr Obama said the move pre-dated Russia's military intervention.
Russian president Vladimir Putin earlier robustly defended his country's military strategy at his first press conference since the crisis began. He said he would only invade Ukraine as a last resort.
President Obama acknowledged that Russia had legitimate interests in Ukraine but said that did not give Mr Putin the right to intervene militarily. He said: "President Putin seems to have a different set of lawyers making a different set of interpretations. But I don't think that's fooling anybody."
US Secretary of State John Kerry later paid tribute to pro-Western demonstrators killed in Kiev's Independence Square.
Mr Kerry, who was mobbed by crowds in a visit to the square, described the experience as "incredibly moving".
Meanwhile, Foreign Secretary William Hague disowned a leaked document suggesting the UK should not impose trade or financial sanctions on Russia.
Mr Hague told MPs that the note - photographed being carried by an official into Downing Street - would "not necessarily" inform decisions as he came under pressure from Labour to outline what steps the UK would take.
In Crimea, Russian forces fired warning shots in a confrontation with Ukrainian servicemen at an air base, and Russian navy ships were reported to have blockaded the strait separating the Ukrainian Black Sea peninsula from Russia.
Mr Putin said Russia reserved the right to use all options to protect compatriots who were living in "terror" in Ukraine, but force was not needed for now.
His comments eased the pressure on Russia's stock markets, which had crashed on Monday.
Mr Putin denied the Russian armed forces were directly engaged in the bloodless seizure of Crimea, saying the uniformed troops without national insignia were "local self-defence forces".
He said: "As for bringing in forces, for now there is no such need, but such a possibility exists. What could serve as a reason to use military force? It would naturally be the last resort. Absolutely the last."
Mr Putin said there had been an unconstitutional coup in Ukraine, and Viktor Yanukovich, who fled to Russia last week, was still the legitimate leader. No Ukrainian government elected "under such terror as we see now" would be legitimate, he said.
Mr Putin warned that Western sanctions under consideration against Russia would be counter-productive as the US looked to impose them within days. Moscow said it would retaliate.
Mr Kerry, on his first visit to Ukraine since the overthrow of Russian-backed President Victor Yanukovich, met interim leaders and announced a $1 billion economic package and technical assistance for the government.
In the Commons, Labour's shadow foreign secretary Douglas Alexander urged Mr Hague to set out what steps the UK would take.
Mr Alexander warned: "I am afraid that the United Kingdom's words will count for little without more credence being given to these options and a willingness at least to countenance their use in the days and weeks ahead."
Mr Hague told the Commons that Russia would suffer "significant costs" if it did not pull back from Ukraine. He added that the UK Government was "considering a wide range of options here, and I haven't ruled any option out".
Mr Hague also said the invasion could have been planned for a long time, announced financial help for Ukraine, backed sending UN monitors and said the use of Russian "agent provocateurs" could not be ruled out.
Deputy Prime Minister Nick Clegg has also denied that ministers are seeking to limit EU sanctions on Russia to exempt the City of London.