About 100 demonstrators burned tyres and threw stones at riot police who responded with tear gas and water cannons on Wednesday in Tizi-Ouzou.
At least a dozen people were detained, said witnesses. There were no reports of injuries.
Most shops were closed in Tizi-Ouzou, the main city in Kabylie about 90km from the capital Algiers. Some Berbers had called for demonstrations and a strike to coincide with Bouteflika's first visit to the region since 1999.
Bouteflika is a favourite to win another five-year term on 8 April and seeks support of the Berber ethnic minority, many of whom boycotted parliamentary elections in 2002.
His trip to Tizi-Ouzou, a city also hard hit by separatist violence in the past decade, was symbolic and many political analysts had not expected him to make it.
The crisis in Kabylie was sparked by the death of a school boy in police custody in April 2001. In ensuing riots more than 100 people died and thousands were injured.
Wednesday's street disturbances began as Bouteflika was delivering a speech, in which he made no reference to the Berbers' main demand of making Tamazight an official language, alongside Arabic.
Talks between the government and Berber activists broke down earlier this year after Bouteflika refused to make the Berber language an official one, insisting instead on a referendum.
"They're all mafia, Bouteflika has not come here in three years when 100 people died and now he comes for his election campaign," said Gaya, a young man in his early 20s.
Berbers, the original inhabitants of North Africa before the 7th century Arab conquest, want more language, cultural and democratic rights in Algeria. They make up a fifth of the country's 32 million people.