Scuffles broke out when several hundred protesters, including some leftist politicians, tried to breach police barriers at the border where Austria has said it will toughen controls in response to migrant and refugee flows into Europe.
The marchers wore orange life jackets in a sign of solidarity with the thousands of African and Asian migrants who have drowned trying to cross the Mediterranean, and brandished a large banner with the slogan 'People Over Borders'.
One demonstrator was arrested, prompting a sit-down protest in front of the police lines by fellow marchers demanding his release, but no injuries were reported.
Austria said this month it would introduce tougher controls at the pass from June 1 at the latest. Italy says the plan breaches EU rules on the free movement of people.
The EU said last week it was assessing the complaint.
The Brenner Pass is the most important Alpine crossing for heavy goods traffic and the controls, if introduced, would slow Italy's main transport link to Germany, its top trading partner.
On Sunday Austria's far right won more than a third of the vote in the presidential election and will face an independent in next month's run-off, dumping out the country's two main parties from the post for the first time.