The pair married in Rome, Italy, in 2012 after a whirlwind romance that started when Jess asked the veteran TV presenter for help kick starting her career.
The BBC handyman, who recently appeared in a Comic Relief special with Royals Prince William and Prince Harry, has released a statement to The Mirror; 'It is with sadness that we announce we are separating. Our focus continues to be the happiness of our son Eddie.'
The couple have an 18-month-old son together, Edward (Edwin) Knowles, who was born in September 2014.
After his birth, Nick told Hello! magazine; 'I am still very much in love with Jessica and we're very much a couple. Our relationship as man and wife is very important to us.
'But on top of that we now have this blissful layer of being Mum and Dad and it's wonderful.'
The 53 year old initially faced controversy over the relationship and his 25-year-age gap with Jessica, 28.
Nick has three other grown-up children from a previous relationship in the 1990s - Charlie, Tuesday and Tyrian-J.
The couple, who own an antiques shop in Eton, had relocated to Andalusia in Spain in 2014 after Nick suffered a series of stress-related health problems including a ruptured artery in his sinus, which caused heavy bleeding.
The father-of-four told Hello! magazine; 'I've always lived my life at a million miles an hour and pushed myself hard.
'But it had got to the point where I knew the balance of my professional and personal life wasn't right. I was trying to be in so many places, I had so many plates spinning and the pressure was getting on top of me.'
The move to Spain was an attempt to achieve a healthier and slower-paced lifestyle.
In April 2007 the Middlesex-born TV star was diagnosed with tuberculosis, which he believes he contracted whilst filming in Zambia for Comic Relief.