Meningitis and septicaemia cases caused by meningococcal group B (MenB) have nearly halved in eligible infants over the last year, according to official figures.
Public Health England (PHE) research has found that the new vaccine has cut the number of new infections in infants under the age of one by 42%. Infants are most likely to contract the potentially deadly MenB before their first birthday.
Only 37 cases have been recorded in the eligible age group since the programme began; this compares to an average of 74 cases in the same period from the previous four years.
All newborn babies in the UK are now routinely offered the jab against MenB in the world's first infant programme using this vaccine.
Protection against any MenB infection was shown to be very high with the vaccine, with disease rates in vaccinated children less than one fifth of the rate in unvaccinated infants.
While MenB is rare, with between 400 and 1,200 cases each year in England, meningococcal infection is the leading cause of meningitis and a deadly form of septicaemia (blood poisoning) and around one in every 10 people affected dies.
There are effective vaccines against other strains, but until now there has been no vaccine proven to offer children protection against MenB.
Dr Mary Ramsay, Head of Immunisation at PHE, said: "This is without doubt great news. MenB is a rare, but terrible disease. It's cut many lives short and can leave children maimed for life, causing devastation for their families. Now we know this vaccine can and will save lives and prevent lifelong disability.
The programme is still in its early days, so we will be monitoring the longer-term impact of the vaccine through our surveillance programme. But the benefit of the vaccine is clear. We hope countries around the world looking at these results will consider introducing similar vaccination programmes, hopefully saving the lives of many, many children."
MenB can cause meningitis, an infection of the membranes that surround the brain and spinal cord, and septicaemia or blood poisoning, both potentially fatal illnesses.
With early diagnosis and antibiotic treatment, most children make a full recovery, but it is fatal in one in 10 cases.
About one in 10 of those who survive are left with severe long-term problems, such as limb loss, and one in three have less serious problems including deafness and learning difficulties.
The vaccine is offered as three jabs; the first at two months, a second at four months and a final booster at 12 months.
PHE monitoring found that over 95% of babies got their first jab and almost 90% the second jab by the age of six months.
Ramsay added: "Infants are most at risk during their first year, so we urge parents to make sure their babies get the first two jabs on time to give them the best protection.
"Call your GP to make an appointment if you've missed any doses. However, not all strains of MenB are covered, so we encourage all parents and older children and adults to be aware of the symptoms.
"The disease develops rapidly. Early symptoms can be confused with flu or other less serious infections. At a later stage children may have pale, blotchy skin and a red rash which doesn't fade when a glass is rolled over it; a sign many parents will recognise.
"However, don't wait to see if a rash develops, parents should trust their instincts if their child appears be getting worse and seek urgent medical attention immediately."