The decline was in line with economists' expectations of a 1.3% drop.
Year-over-year appreciation was 10.4 percent, but this reflects stronger conditions in late 2021.
The figure was down from 13.1% in August.
The broader measure of home prices, the U.S. National Index, fell a seasonally adjusted 0.8% in September.
On a monthly basis, all 20 cities experienced declines, with the West leading the way.
Sales were strongest in Miami, Tampa and Charlotte.
Year-over-year increases in home prices peaked about six months ago and have since declined.
Sharply rising mortgage rates have made home prices more unaffordable, putting many buyers on the sidelines.
Economists believe that home prices have yet to fall further.
Federal Reserve officials don't seem too worried about the process devolving into a deep recession.
"There is still plenty of room for home prices to fall before they can fully adjust to the ongoing collapse in demand," said Ian Shepherdson, chief economist at Pantheon Macroeconomics.
Stocks are set to open modestly higher Tuesday.
The yield on the 10-year Treasury note rose to 3.73 percent.