Prices over the 12-month stretch rose 8.1 percent in the 20-city composite index and 7.3 percent in a 10-city index, the report said.
The sharpest gain in prices was in Phoenix, which led the nation with a 23.2 percent price gain.
Compared to December, 19 of the 20 cities monitored showed a faster rate of price inflation in January. Detroit was the only city to show prices rising at a slower rate than they were rising in December.
New York City joined the rest of the pack with prices in positive territory for the first time after 28 months of negative annual returns, the report said.
"The two headline composites posted their highest year-over-year increases since summer 2006. This marks the highest increase since the housing bubble burst," said David Blitzer, chairman of the Index Committee at S&P Dow Jones Indices.
"Economic data continues to support the housing recovery. Single-family home building permits and housing starts posted double-digit year-over-year increases in February 2013. Despite a slight uptick in foreclosure filings, numbers are still down 25 percent," Blitzer said.
Double-digit annual increases in January were posted in Phoenix, up 23.2 percent; San Francisco, up 17.5 percent; Las Vegas, up 15.3 percent; Detroit, up 13.8 percent; Atlanta, up 13.4 percent; Los Angeles and Minneapolis, up 12.1 percent; and Miami, up 10.8 percent.