Mr Abbott told Mr Putin that Australia was in possession of information that clearly pointed to Russian involvement in the rebel attack that downed the plane in Ukraine.
If true it "would be a very serious matter", he said.
The prime minister pointed out that when the US inadvertently shot down a civilian aircraft, it had duly apologised and made appropriate restitution.
He "commended the precedent" to Mr Putin, the prime minister's office said in a summary of the meeting.
Mr Abbott was referring to Iran Air flight 655, which the US accidentally shot out of the sky in 1988, killing all 290 people on board.
The US expressed deep regret over the tragedy but never formally apologised.
It's not really known what Mr Putin - recently named most powerful man in the world by Forbes magazine - said in response to Mr Abbott's comments.
But the prime minister's office says both men "agreed that all relevant information should be provided to the independent investigation".
Tony Abbott and Vladimir Putin had a tense 15-minute meeting on the sidelines of the Apec summit. Photo / AP
The meeting at the picturesque Yanqi Lake just outside Beijing followed a brief exchange on Monday night, in which Mr Abbott also raised the attack.
Mr Abbott famously promised to "shirtfront" the Russian president over Moscow's involvement but subsequently toned down his language.
He later pledged the pair would have a "robust" conversation - and it appears they did.
Mr Abbott was keen to get the meeting out of the way in Beijing so as not to distract from the economic agenda of the G20 in Brisbane this weekend.
The prime minister also attended a Remembrance Day ceremony on Tuesday and had meetings with the leaders of Mexico and South Korea.
At the summit, he spoke about his G20 plans and free trade agenda.
Mr Abbott leaves Beijing on Wednesday bound for regional security talks in Myanmar, formerly known as Burma. He returns to Australia on Friday.
US President Barack Obama also had about 15 minutes with Mr Putin on Tuesday. The pair discussed Ukraine, Iran and Syria, according to the White House.
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- AAP