She said that the interim government was "pretty much in control of the whole country", but warned that there could be more violence if Bakiyev tried to stay in office.
Anger bubbled over on Wednesday at Bakiyev's administration for rampant corruption and hikes in utility rates, sparking violent protests that forced him to flee the capital for the south of the country, where he retains support.
At Saturday's memorial services, Otunbayeva told the crowd that "those who died on April 7 are the heroes of Kyrgyzstan".
"It was our duty to establish justice. Those who are being buried here today are all our children, the children of Kyrgyzstan," she said.
But as 16 bodies were lowered into graves at the Ala-Too Square ceremony, the Kyrgyz health ministry said three more people had died of wounds received on Wedneday.
"Three people died overnight of their injuries," Damira Niazalieva, the interim health minister, was quoted by local news agency Akipress as saying.
The total number of dead currently stands at 79, with up to 1,500 people reported to have been injured in overall unrest.
The interim government says it plans to stay on for six months before holding elections.