Munfiatun, the 28-year-old wife of Malaysian terrorist suspect Noordin Mohamed Top, was arrested in September.
Noordin is one of the suspected masterminds in the Bali bombings and other recent attacks in Indonesia.
Munfiatun, also known as Fitri, was convicted on Thursday of hiding information about her husband by changing Noordin's name to Abdurahman Aufi on the couple's wedding documents after they were married last year, and for failing to turn him in to authorities.
"The defendant has been legally proven to have hidden information about a perpetrator of a terror action," Chief Judge Amiryat told the court.
"Because the defendant has been proven guilty, then the Bangil District Court has to sentence the defendant to three years in prison."
Munfiatun said nothing as the verdict in the District Court of Bangil was read. Earlier, she had confessed that she knew Noordin was a suspect and that she tried to conceal his identity.
After the hearing, attorneys for Munfiatun said they would appeal the verdict.
"The defendant has been legally proven to have hidden information about a perpetrator of a terror action"
Chief Judge Amiryat
Munfiatun was taken to a prison in Bangil, located about 900km east of capital Jakarta.
Noordin and another Malaysian, Azahari bin Husin, are suspected masterminds in a series of bomb attacks in Indonesia, including the Bali blasts that killed 202 people on 12 October 2002; the bombing of the JW Marriott hotel in 2003; and the September 2004 bombing outside the Australian embassy in Jakarta that killed 10 people.
The two men are believed to be somewhere in Indonesia.