It was the second consecutive report in which prices rose in all but one of the monthly study's monitored cities. For September, prices rose in every market in the report, except Chicago. In the prior report, only Seattle bucked the trend.
It was also the sixth consecutive month of price gains.
Increases were slight in Washington, Tampa, Fla., Boston, Detroit and Charlotte, N.C., in the month, but overall prices rose 3 percent, just above the consensus prediction of 2.9 percent and significantly better than the 0.8 percent rise in the previous report.
In a separate report, the Federal Housing Finance Agency said home prices rose 1.1 percent from the second quarter to the third in a seasonally adjusted price index that tracks homes with mortgages backed by either the Federal National Mortgage Association or the Federal Home Loan Mortgage Corp., better known as Freddie Mac and Fannie Mae.
From the third quarter of 2011 to the third quarter of 2012, prices among those FHFA tracks rose 4 percent on a seasonally adjusted basis.
"The past year has seen consistent price increases, but a number of factors continue to affect the recovery in home prices such as stagnant income growth, high unemployment levels, lingering uncertainty about the macroeconomy, and the large number of homes in the foreclosure pipeline," said FHFA economist Andrew Leventis.