The 0.1% increase between the two quarters was the first quarterly rise since Quarter 1 2010.
The more volatile monthly figures showed a 0.5% decline in prices in September.
This continued the mixed monthly picture experienced so far this year with four rises, four falls and one no change since January.
This mixed pattern is consistent with a market where prices are lacking genuine direction.
Housing economist Martin Ellis said: "Greater uncertainty about economic and personal financial circumstances, together with pressure on householders’ finances from weak earnings growth, higher inflation and increases in taxes, are likely to be constraining housing demand.
"Despite these pressures, low interest rates and a rise in employment over the past year, have been supporting the market, resulting in broad stability in both prices and activity.
"We expect little change over the remainder of this year."
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