The accord was signed on the sidelines of the Black Sea Economic Cooperation meeting in Istanbul. Moscow imposed a raft of sanctions against Ankara after Turkish jets downed a Russian warplane over the Syrian border in 2015.
Russia agreed on Monday to lift remaining trade sanctions against Turkey imposed after Turkish air forces shot down a Russian warplane over the Syrian border in 2015.
Turkish Deputy Prime Minister Mehmet Simsek and his Russian counterpart Arkady Dvorkovich signed the accord on the sidelines of a summit of Black Sea regional leaders in Istanbul on Monday.
It said that the document was an important step towards the normalisation of economic relations and increasing trade volumes.
Delegates from 12 member states attended the twenty-fifth anniversary summit of the Black Sea Economic Cooperation Organisation (BSEC), which discussed economic cooperation and institutional reforms.
BSEC members include Albania, Armenia, Azerbaijan, Bulgaria, Georgia, Greece, Moldova, Romania, Russia, Serbia, Turkey and Ukraine.
Turkish tomatoes expected to re-enter Russian kitchens
The Russian government in a statement confirmed that the document "on the lifting of bilateral trade restrictions" was signed in the presence of Turkish Prime Minister Binali Yildirim and Russian Premier Dmitry Medvedev.
There were no immediate details on the contents of the document, but it is expected to again allow the import to Russia of tomatoes, a key Turkish agricultural export.
The November 24, 2015 shooting down of the Russian plane led to an unprecedented crisis in ties and prompted Russia to impose a raft of sanctions against Ankara.
These included an effective ban on Russian package holidays to Turkey, ruining the 2016 tourism season in the country's south. That ban has since been lifted.
It was the first time a NATO member downed a Russian warplane since the 1950s, going back to the days of the Korean War.
After a reconciliation deal in summer last year, relations have seen a rapid improvement with the two sides working together in a bid to end the Syria conflict.
Erdogan stresses on sustainable development
Earlier, Turkish President Recep Tayyip Erdogan told the summit delegates that Turkey will continue to support "all future works" in the Black Sea region.
Erdogan said that BSEC can "lead the way" with regards to exerting more efforts on sustainable development in the region.
"It is up to us, the member states, to make efforts to reinforce our cooperation under this umbrella. Here in Anatolia, we have a saying: a neighbour needs even the ash of another neighbour," he said.