Prices were up to 5.4% compared to the same quarter in 2015 - in the previous four quarters the annual rise was more than 7%.
Compared to the second quarter of this year, prices were almost flat, rising by just 0.8%.
The figures are from the NI Residential Property Price Index, which analyses almost all sales, including cash deals.
The average standardised price, across all property types, is just over Â£124,000.
The biggest annual rise in the third quarter was in the Antrim and Newtownabbey council district where prices were up by 7.3%.
The smallest annual rise was in Ards and North Down where prices were up by 2.1%
Among property types the biggest annual rise was for terraces, up by 7.1%.
The smallest annual rise was for apartments which were up by 4%.
The number of deals completed in the third quarter was 5,200.
House prices in Northern Ireland continued to rise in the third quarter of this year, but at a slower rate.