The vaccine, Rotarix, will halve the number of vomiting and diarrhoea cases caused by the bug, and there could be 70% fewer hospital stays as a result, it has been estimated.
The programme will see children under four months vaccinated against rotavirus, which causes thousands of diarrhoea cases a year in under fives.
About one in five children who catch it require medical attention and one in ten then end up in hospital, according to the Department of Health.
The vaccine is already used to routinely vaccinate children in the USA and several other countries.
Rotavirus-related hospital admissions have fallen by as much as 86% in the USA since it was introduced.
The immunisation programme will begin on 1 July.
Children will need two doses, administered as a small amount of liquid into the mouth, given at two and three months of age.
Minister Poots said: "Rotavirus spreads very easily and affects thousands of children every year, causing distress for them and their families.
"Immunisation of every child is vital to prevent illness and protect life. I would encourage all parents of young children to avail of this vaccine when the programme begins in July."
Dr Michael McBride, NI Chief Medical Officer, said: "Rotavirus is the most common cause of diarrhoea in young children and this vaccine will protect our children and reduce hospital admissions for serious rotavirus infection.
"Many people think of diarrhoea as something that all children get and that you have to put up with. But there is a way to protect children from this."
The vaccination programme will be closely monitored by the Public Health Agency, and Medicines and Healthcare products Regulatory Agency (MHRA).
The DUP minister has also announced a change to the current arrangements for protecting children against meningitis C.
From 1 June, a new teenage booster injection given in school will replace the booster that is currently given at four months old.
A statement from the Department of Health said: "Current evidence shows that the four-month booster is no longer required.
"The teenage booster vaccination will be offered during the 2013/14 school year."