Mr Yanukovych flew from China to Sochi in southern Russia for the meeting. He also cancelled a visit to Malta.
Last month he shelved a partnership deal with the EU, triggering angry protests in Ukraine's capital Kiev.
Jailed opposition politician Yulia Tymoshenko has reportedly called off a prison hunger strike.
The former prime minister's daughter, Eugenia, said her mother had accepted a request from protesters in Kiev to stop the fast.
She had reportedly begun the hunger strike on 25 November in protest at Mr Yanukovych's failure to sign the EU deal.
Thousands of anti-Yanukovych protesters remain outside the government building on Kiev's Independence Square, braving bitter cold.
They are furious that he made an 11th-hour U-turn in relations with the EU, refusing to sign the association agreement that had been prepared during years of negotiations.
In Sochi, Mr Yanukovych discussed "preparation of a future treaty on strategic partnership" with Russia, his press service said.
The talks covered various economic issues, the statement said, without elaborating.
Mr Putin has been urging Ukraine to join Russia's customs union with Belarus and Kazakhstan - a union whose entry terms are far less demanding than the EU's.
In recent months Russia has put Ukraine under economic pressure, imposing long customs delays at the border and banning imports of Ukrainian sweets.
Arseniy Yatsenyuk, a Tymoshenko ally and leader of the main opposition faction in parliament, condemned the talks in Sochi.
"Their attempts to sell Ukraine to Russia have not ended in any way," he said.  "If Yanukovych tries to sign anything with Russia about the customs union it will lead to a bigger wave of protests."

28 December 2015 Last updated at 20:11 GMT
The woman's husband was rescued from the blaze and is being treated in hospital.
Clodagh Rice has been to the scene.

Kleptomaniac Theo, from Ipswich, first hit the headlines in 2013 for stealing Christmas decorations.
Recently he has been stealing toy food, including a pineapple and an aubergine.
"We are deeply ashamed of our cat, especially as he had convinced us that he had changed his criminal ways," his owner wrote to neighbours.
Rachael Drouet created a leaflet for her neighbours in a bid to reunite the stolen items with their rightful owners.
"This year has been relatively quiet, save for some Bettaware catalogues and the odd flat balloon," the leaflet read.
"Until a few days ago when he started bring home toy food.
"So far we have cheese, a green pepper, fish, a pineapple, an aubergine, and a felt basket to put them all in."
Theo, a five-year-old Siamese cross, also managed to bring home a child's body warmer.
Earlier this year, he stole a catalogue from a house down the street owned by a policeman, which Ms Drouet said "wasn't ideal".
Among the items stolen in the last couple of years are muslin cloths, fluffy pens, a USB phone charger cable and a child's piece of art.
Theo also took to stealing Christmas decorations from neighbours' trees.
Ms Drouet said this year she managed to reunite items from Theo's haul with their rightful owners before too long.
"I wrote the flyers and then luckily managed to find out who all the things belonged to," Ms Drouet said.
"You get tired of knocking on neighbours' doors and saying 'me again'".
Ukraine's President Viktor Yanukovych and his Russian counterpart Vladimir Putin have held surprise talks on a "strategic partnership treaty".
[NEXT_CONCEPT]
An elderly woman has died in a house fire in Enniskillen.
[NEXT_CONCEPT]
A pet cat with a track record for stealing has slipped back into his criminal ways despite convincing his owner he was a reformed character.