The meningitis B jab is being offered on the NHS for infants aged two months, followed by a second dose at four months and a booster at 12 months.
There will also be a temporary catch-up programme for babies who are due their three and four-month vaccinations throughout September.
The scheme, which has been delayed by cost disputes, is the first national and publicly-funded programme against the infection in the world.
The jab will protect against infection by meningococcal group B bacteria, which can cause meningitis and septicaemia (blood poisoning).
While meningitis B can affect people of any age, it is most common in babies and children under five.
Tests suggest that the new vaccine, called Bexsero, will protect against around 90% of the meningococcal group-B bacteria strains circulating in the UK.
Around 1,200 people - mainly babies and children - get meningitis B each year, with around one in 10 dying from the infection and others left with permanent disabilities.
Christopher Head, chief executive of the Meningitis Research Foundation, said: "We hope this vaccine will save many lives and spare countless families the trauma of seeing a loved one die or become seriously disabled because of meningitis B.
"If cases continue as they have in the past, over the next decade this vaccine could potentially prevent up to 4,000 cases of meningococcal disease in children younger than five in the UK.
"However we must remind the public that there are still some forms of the disease which are not covered by vaccines, so it is vital that people are still aware of the symptoms of meningitis and septicaemia."
One of the first babies to receive the new jab is the granddaughter of a lifelong meningitis campaigner.
Dr Jane Wells, 58, of Stroud, will see her granddaughter, Daisy, born on May 29, vaccinated against the infection as part of the first round of catch-up jabs.
Dr Wells co-founded the charity now known as Meningitis Now, after her son Dan suffered meningitis as a baby and teenager.
She said: "I'm so pleased that Daisy will benefit from the vaccine, it's the perfect gift.
"Meningitis has been prominent in our family - we have experienced three deaths and my son, Dan, survived the disease twice. With our history, we were very worried for Daisy."
Mr Wells caught meningitis aged two and again when he was 13.
"When Dan first contracted meningitis it completely changed our lives - we were in a dark hole and no one could tell us anything," Dr Wells said.
"No parent or child should have to go through what we did. Dan struggled with his balance, tiredness, sickness and his education for years but luckily his after-effects were minor compared to what they could have been.
"Fortunately, when Dan contracted the disease a second time, treatment and recognition had improved drastically."
Sue Davie, chief executive of Meningitis Now, said: "Whilst reaching this milestone is great news, I urge all parents to remain vigilant of the signs and symptoms of meningitis. There are still types for which there is no vaccine available."
Another meningitis vaccine - Men ACWY - is currently being offered to 17 and 18-year-olds and students starting university this year.
Symptoms of meningitis develop rapidly and include a high fever with cold hands and feet, vomiting and refusing to feed, agitation, drowsiness or being floppy or unresponsive.
Grunting or breathing rapidly or having an unusual high-pitched or moaning cry are other signs.
Some babies develop a rash that does not fade when a glass is rolled over it.