HMS Triumph fired missiles at targets in Afghanistan as UK forces participated in the military operation against Osama Bin Laden's al-Qaeda terrorist organisation.
The attack was part of the first wave of missile strikes and was concentrated on a training camp.
The crew's families were joined by Adam Ingram, Minister of State for Armed Forces and the Commander-in-Chief-Fleet, Admiral Sir Alan West, to welcome the vessel home on Monday.
The Trafalgar class nuclear-powered submarine, with a crew of 130, is one of three Royal Navy submarines closely involved in Operation Veritas.
For two years the sub has been engaged almost continuously in the Far East, the Arabian Sea and the Mediterranean.
Soon after the war against terror was declared, HMS Triumph was diverted at short notice to the Indian Ocean.
There it joined with coalition forces for operations against al-Qaeda and the Taliban within Afghanistan.
Mr Ingram said: "I am delighted to be able to welcome HMS Triumph home today.
"She has played a vital part in the international coalition's effort against terrorism and Britain is justifiably proud of the dedication and commitment she has displayed.
Many changes
"Over the past year much of the flotilla has been under repair and HMS Triumph has carried significant additional tasking.
"The ship's company has risen to the challenge and has borne the many changes of programme with fortitude, commitment and professionalism.
"I would thank all those families and loved ones who have similarly had their lives so disrupted."
He added: "We should never forget those that stay at home and I would wish the commanding officer, ship's company and all their families, a very merry Christmas and pass on the country's thanks for a job very well done."