"In the light of the circumstances... The chamber does excuse Mr Ruto from the proceedings before the court... For one week only," Judge Chile Eboe-Osuji said at an urgent hearing.
Ruto is the highest-ranking serving official to be tried by the ICC, and is the first suspect to be excused to go home to work in the history of the 10-year-old court.
He left the court and went to the airport to fly back to Kenya to deal with the ongoing hostage crisis at Nairobi's Westgate shopping mall, where at least 69 people have been killed and another 63 are reported missing.
Ruto's lawyer Karim Khan, who had asked for his client to be excused for two weeks, told the judge that Ruto wanted to catch a flight to Kenya leaving today morning.
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"The world would have found it intolerable if the US president and deputy president wasn't there after 9/11," Khan told the court.
"Well, this is Kenya's 9/11."
Ruto is in The Hague on charges of masterminding some of the 2007-08 post-election violence in Kenya that left over 1,000 people dead and several hundred thousand displaced.
Prosecutor Anton Steynberg argued that only a one-week adjournment was necessary for Ruto to put people in place to deal with the Nairobi crisis.
"It's really a very trying moment for our country," Ruto said outside the court after the judge excused him.
Even before the Nairobi militant attack, the court was weighing whether to excuse Ruto from large portions of his trial so he can perform his official functions.
Ruto has also already asked for his trial to be held nearer to home, in Tanzania or Kenya, something the court has so far rejected.
"Both myself and the president have committed ourselves to be present here in court so that we can clear our names, but we have to counterbalance our responsibilities and legitimate requirements to 40 million Kenyans," Ruto said.