Widow Rita Schwerner Bender said the verdict was a "first step"
The 80-year-old former Ku Klux Klan man was convicted of manslaughter and recruiting the killers by a jury of nine whites and three blacks.
Killen now faces up to 20 years in jail for the role he played.
Rita Schwerner Bender, widow of victim Michael Schwerner, said the conviction was a "very important first step".
But she asked why the jury "could not bring themselves to acknowledge that these were murders, that they were committed with malice".
Michael Schwerner's widow added that the state of Mississippi was "complicit in these crimes and all the crimes that occurred" and called for a further inquiry.
I believe we proved murder
Mark Duncan
prosecutor
Bennie Thompson, the state's only black congressman, said justice had "finally arrived in Philadelphia".
Ben Chaney, brother of James Chaney, the only black man among the three victims, thanked prosecutors and said he sensed "hope".
District Attorney Mark Duncan said he still believed the prosecution had "proved murder".
Clearly referring to the Alan Parker 1988 film Mississippi Burning about the struggle to bring the killers to justice, he added: "We won't be painted or described or known throughout the world by a Hollywood movie any more."
No emotion
The jury in Mississippi rejected the murder charges against Killen but did find him guilty of recruiting a mob to kill the three.
His wife, Betty Jo, went to her husband with tears in her eyes and hugged him.
Ray Killen sat in a wheelchair and wore a breathing tube while in court
As he was wheeled away, he struck out at two television microphones and a TV camera.
The defendant had denied taking any part in the killings of Mr Schwerner, 24, Mr Chaney, 21, and Andy Goodman, 20.
A Baptist preacher, he showed no emotion as the verdict was read in the courtroom.
He used a wheelchair in court and was connected to breathing apparatus during the trial.
Killed and buried
The activists were two white men from New York and a local black colleague, who were killed while campaigning for the registration of black voters.
They were arrested for a dubious traffic violation, and attacked by a gang of Klansmen and police after being released in the middle of the night.
They were abducted as they drove out of the Mississippi town and shot dead.
Their bodies, riddled with bullets and badly beaten, were buried at a dam and only found 44 days later after an extensive search.
Killen, who was a suspect in the original investigation but never convicted, was re-arrested after new evidence emerged.
Ku Klux Klan members in disguise
Edward Killen, an 80-year old former Ku Klux Klan member, was convicted of three counts of manslaughter today for the murder of three civil rights workers exactly 41 years ago this very day.

Michael Schwerner, 24, Mr Chaney, 21, and Andy Goodman, 20, were killed in 1964. Killen was originally a suspect and was rearrested when new evidence emerged. 

Killen now faces twenty years in jail. He was cleared of carrying out the murder, but convicted of recruiting a gang of Klansmen and police, who abducted the three men, shot them and beat them to death before burying them in a dam.