Lavrov and Yang Jiechi signed the agreement on the first day of Lavrov's two-day visit to China. The Russian foreign minister is also set to meet with Chinese President Hu Jintao and the country's premier, Wen Jiabao, during his trip.
The signing of the agreement, Lavrov said, brought an end to "more than 40 years of negotiations."
Earlier this month, a senior Russian security official said that Russia would relinquish control of the Tarabarov Island and about half of the Bolshoi Ussuriysky Island, located at the confluence of the Amur and the Ussuri rivers, under a 2004 bilateral agreement.
The 2004 agreement on the eastern sector of the 4,300-kilometer (2,700-mile) border, the world's longest land frontier, was signed after China agreed to drop territorial claims to islands near the Russian city of Khabarovsk.
The two islands, occupied by the Soviet Union in 1929, were the site of several border skirmishes between the two powers during the 1960s.
Russia and China signed border agreements in 1991 and 1994 delimiting the eastern and western sections of their frontier, but issues over several minor sectors were left unresolved.