Gary Karr, 52, was charged with extortion and kidnapping and could face a sentence of life in prison. O'Hair, her son Jon Garth Murray and her granddaughter Robin Murray O'Hair disappeared from San Antonio in 1995 along with $500,000 in gold coins.
Although federal prosecutors named two other suspects, Karr was the only one charged.
The decision caps a two-week long trial that saw testimony from 68 witnesses, four of whom appeared for the defense. Karr did not take the stand.
Although he was found innocent of of involvement in the actual kidnapping, he was convicted of conspiracy in the robbery and extortion of the family for money.
The eight-man, four-woman jury began its deliberations Tuesday.
Jurors had to grapple with a small mountain of evidence, as they mulled five separate charges lodged against Karr in connection with the abduction and robbery of the O'Hairs.
Charges included conspiracy to kidnap the O'Hairs; conspiracy to commit robbery and extortion of the family's property; traveling interstate to commit violent acts resulting in the death of a person; conspiracy to profit financially from criminal acts; and transportation of stolen property across state lines.
The Murray O'Hairs are presumed dead, although their bodies have not been located, and no one has been charged with their murder.
Earlier Friday, jurors informed Judge Sam Sparks that they were unable to reach unanimous agreement on all of the indictment counts. The judge ordered them to return to their deliberations, and the final decision came minutes later.
Madalyn O'Hair and her family disappeared from San Antonio in 1995 along with $500,000 in gold coins. Some at the time advanced theories that she may have suffered from a terminal illness, or that the family had deliberately absconded with money from an atheist group.
Federal investigators, though, pieced together a tapestry of evidence indicating that the O'Hairs were kidnapped, robbed and then killed. Their bodies are believed to have been dismembered and put into 55-gallon drums and then buried, according to those close to the case.