The two men had a 15-minute meeting on the sidelines of the APEC summit late on Tuesday, during the leaders' retreat at Yanqi Lake outside Beijing.
It was their second conversation in 24 hours after Mr Abbott approached the Russian leader informally at the APEC gala dinner on Monday night.
Their Chinese host seated them beside each other at the opening plenary session, where they appeared less than friendly.
Australian government sources say the Prime Minister told Mr Putin later that Australia had reliable evidence that it was a Russian missile fired from Eastern Ukraine which shot down the airliner and that the launcher had then crossed the border into Russia.
He is understood to have said that when the United States had shot down a civilian aircraft in error, it had apologised and made restitution.
He's believed to have told the president he should follow that example.
The sources said the leaders agreed that the international investigators should be given all relevant information and assistance in line with UN Resolution 2166.
The Russian Government's assessment of the meeting is not yet known.
