That's a huge fall from the 2.7 per cent rise between July and August.
The figures, by Halifax, showed prices in the three months to September grew two per cent, down from three per cent in the three months to August.
On a yearly basis, prices rose 8.6 per cent on September last year, down from nine per cent in August - suggesting the much-anticipated post-summer bounceback has yet to take place.
The measure also showed the price of flats were rising faster than houses - prices of apartments have risen 60 per cent over the past 10 years, significantly higher than the 38 per cent average for all residential properties.
Detached homes, meanwhile, have risen 21 per cent, while bungalows have risen 28 per cent.
Halifax pointed out that while using a month-on-month measure of house price movements can be volatile, "increasing demand is combining with very low supply to drive robust underlying house price growth.
"There is little reason to expect any fundamental shift in the key market drivers over the coming months."