Scottish newspaper The National had listed a number of posts in an article last year including one in which Mr Houghton argued that while there was "no credible evidence to suggest the Holocaust did not happen" he went on to say: "I do find some of the events fabricated."
He was also quoted as having written on a martial arts forum in 2013 that he did not see how homosexuality was good for the human race.
In other alleged comments he said Islam's core teachings had the goal of "world domination" and that some Muslims had big families with the aim of creating "Eurabia".
He released a statement on his Twitter feed at the time, saying the comments were taken "out of context" and insisted he had never held antisemitic, racist or homophobic views.
Mr Houghton said in a statement on Monday: "The comments which led to my suspension were isolated and took place nearly a decade ago.
"They in no way reflect my political or professional record and I find prejudice of any kind abhorrent."
A party spokesman said of the disciplinary committee ruling: "The committee took into account the respondent's unreserved acceptance that what he had done when much younger was wrong and that he understood the consequence of his actions.
"The committee also noted the letters of support for the respondent from local groups."
A Board of Deputies spokesperson said: “We have raised our concerns on this matter with the Conservative Party and are coordinating a response with the Scottish Council of Jewish Communities”
