It was the first time Ruto had been forced to listen directly to court testimony from a victim. He is charged with Joshua arap Sang, a radio executive. Both deny all charges.
Ruto faces three counts of crimes against humanity, including being an "indirect co-perpetrator" of murder, persecution and forcing people from their homes.
Uhuru Kenyatta, Kenya's President, faces similar charges in a separate case due to start in November.
The first witness was hidden from the public gallery by a curtain, her voice was distorted and her face pixilated for screens outside the courtroom.
She said people were forced back into the flames or shot with arrows as they tried to run from the wooden Kenya Assemblies of God church in Kiambaa, in Ruto's support heartland 300km northwest of Nairobi.
The mob was from Ruto's Kalenjin tribe, the witness said. She and those seeking refuge in the church were Kikuyus, the tribe whose political leader, Mwai Kibaki, was said to have stolen the election days earlier. The trials are expected to last several months, or even years.