The battalion suffered the largest number of fatalities of any in Afghanistan
Soldiers recently returned from Afghanistan have been receiving medals at their base in Ballykinler, County Down.
Their six month tour of duty saw 2 Rifles lose 13 men, with 80 injured.
Britain's most senior commander in Afghanistan, General Sir Nick Parker, was present at the ceremony.
He said the deaths of five soldiers after an Afghan policeman opened fire with a machine gun in Helmand Province should not sway overall strategy.
"I hope we don't make strategic decisions on the basis of this low-level, terrible action," he said.
"If you start extracting conclusions from something at that level it could be very damaging.
"I know that the Afghan security forces are part of the future of this country."
Gen Parker's son, Harry, was injured in Afghanistan.
About 500 soldiers received medals on Thursday, with the families of some of those killed were handed the Queen Elizabeth Award.
A key part of their role was mentoring and patrolling alongside the local police and army.
The battalion suffered the largest number of fatalities of any in Afghanistan.
Hundreds of family members and dignitaries stood and applauded the soldiers.
Some soldiers, wearing their desert fatigues, were on crutches and one triple amputee was present.
The battalion, based in the dangerous central Helmand province area of Sangin, found around 200 improvised explosive devices, but also suffered losses and injuries from the deadly bombs.
Rifleman Damien Britton, 23, from Bristol, relived the moment when one of his friends lost his life.
He was driving in a convoy of vehicles when they were attacked with bombs.
"You relive it every day in your mind, but you can't hold on to it. You have to let it go because you are working every day until the end of the tour, you can't let it play on your mind."
A ceremony lasting more than an hour saw the troops receive their medals from octogenarian Field Marshal Edwin Bramall.
He paid tribute to those who lost their lives.
"Thirteen brave and much missed comrades in arms, good men and good friends, we will never forget them, the superb sacrifice they made as true soldiers and warriors," he said.
The commanding officer of 2 Rifles, Lieutenant Colonel Rob Thomson, said his men performed heroically.
"It was the most intense, complex and nuanced fight in my 20 years in the Armed Forces," he said.
"We left Sangin in October 2009 a better place than when we arrived."