Prevnar 13 adds protection against six additional varieties of bacterial infection compared with the current vaccine.
The vaccine, developed by Wyeth, is the first product to win FDA approval since Pfizer acquired that company last year.
With sales of $2.7 billion in 2008, Prevnar was the world's top-selling vaccine in 2008 and was considered a key product in Pfizer's decision to purchase Wyeth for $68 billion.
The FDA was scheduled to make a decision on Prevnar by last September, but extended its review twice since then.
Infections from pneumococcal disease dropped dramatically after the original Prevnar was released in 2000. However, infections began rising again in 2005 with the development of new variants of the disease.
Dr. Emilio Emini, Pfizer's chief of vaccine research, said the six new varieties of pneumococcal disease covered by the vaccine account for 70 to 75 percent of new infections in the U.S. When combined with the seven varieties covered by the original vaccine, Emini says Prevnar 13 covers 90 to 95 percent of the causes of the disease in the U.S.
The vaccine also protects against two varieties of pneumococcal disease that account for most cases in the developing world.
The World Health Organization has called the disease the top vaccine-preventable cause of death in the world.
The vaccine requires a series of four injections, generally given at 2, 4 and 6 months old and then between 12 and 15 months old.
To assure widescale use in the U.S., Prevnar 13 will need the recommendation of the Centers for Disease Control, which issues guidelines on vaccines to doctors and hospitals. The FDA approval announcement came less than an hour before CDC's panel on immunization was set to vote on Prevnar 13 in Atlanta.
Pfizer shares rose 23 cents, or 1.7 percent, to $12.96 in morning trading.