Mr Lowe sued over an August 2004 column by The Times writer Martin Samuel claiming he had "shabbily handled" the suspension of manager Dave Jones in the wake of child abuse allegations in January 2000.
Mr Jones was suspended for 12 months on full pay so he could concentrate on defending the case.
The article about the state of the FA, headed "Men who would be kings are a ghastly alternative", referred to Mr Lowe as a "chairman whose idea of crisis management was to remove his manager over a court case that collapsed within 24 hours".
It went on to ask: "How would Lowe approach the issue of an England player accused of breaking the law, when he so shabbily handled the case of David Jones, his manager?"
Mr Lowe, 47, said he felt the article was a "real blot" on his character. "I'm used to people writing things about me which are very often incorrect and not very nice but that's the hustle and bustle of football - but this was a very grave employment issue and I felt that we, as a club, had behaved extremely well in trying to balance a very difficult situation," he said.
In December 2000, Mr Jones stood trial on 21 charges of sexual and physical abuse of children, arising out of an investigation into a Merseyside home where he was employed as a care worker. Four days into the trial the judge directed an acquittal, and Mr Jones, who maintained his innocence from the start, walked free.
William McCormick, counsel for the newspaper, which pleaded justification and fair comment, said: "This case is about freedom of expression exercised by Mr Samuel - the freedom to write legitimate comment.
"He is a columnist - there to provoke discussion."
Mr Samuel said in evidence that the article represented his honestly-held opinion.
It took a High Court jury three hours to reach its unanimous verdict after an eight-day case before Mr Justice Eady in London.Reuse content