Kosovo police asked for reinforcements after 1,000 Kosovo Serbs, joined by another 150 from across the border, ransacked and burned the two crossings.
Veton Elshani, a Kosovo police spokesman, said there were no casualties as Kfor rushed troops to the two sites in the first intervention since the province declared independence.
Protesters also tipped over metal sheds housing Kosovo's customs service and sent them sliding down a hill and into a river.
"We couldn't do anything. We just moved away, as there were only a few of us compared with the group of very angry Serbs," a Kosovo Serb policeman at the scene told AFP.
Kosovo's declaration brought condemnation from Belgrade, the Serb capital, and has caused divisions among world powers, only some of which have recognised Europe's newest nation.
On Tuesday Taiwan joined those which have officially recognised Kosovo, in a move likely to antagonise China which has expressed "grave concern" over Kosovo's secession precisely because of the signals it could send to Taiwan.
"The Republic of China [Taiwan] from today on formally recognises Kosovo," James Huang, Taiwan's foreign minister told reporters, and stressing that nations had the right of self-determination.
China reacted angrily to Taiwan's expression of support for Kosovo, bluntly telling the island it had no right to offer an opinion on the subject.