The ministry said the soldiers were on routine patrol in Nahr-e-Saraj district when their vehicle hit the bomb Tuesday. The soldiers were members of the Royal Regiment of Scotland.
"They received immediate medical attention and were evacuated by air to the Military Hospital at Camp Bastion but could not be saved," the announcement said.
"Our thoughts are with the families who have lost loved ones in this incident, which underlines the threats faced by our personnel as they continue to hand over security operations to their Afghan counterparts ahead of U.K. combat operations concluding by the end of next year," a ministry spokesman said.
Most of the 9,000 British forces in Afghanistan are based in Helmand.
British Prime Minister David Cameron said the country has paid a "very high price" for its work in Afghanistan, which he said is important "because it's vital that country doesn't again become a haven for terrorists, terrorists that can threaten us here in the U.K.," the BBC reported.
More than 440 British soldiers have died in Afghanistan since the war began in 2001.