Students wearing balaclavas pelted shop windows with rocks near the city's main square and clashed with riot police who fired tear gas to disperse them.
Bogota imposed a curfew in three of the more populated areas of the city after violence continued into the night.
President Juan Manuel Santos, who has been unable to end the so-called national strike that has united potato growers, milk producers and teachers, acknowledged agriculture is in crisis, but called for peaceful dissent while talks about possible solutions are going on.
In a televised address, he said: "The protests are valid but, via dialogue, we will resolve the problems. We are in a storm but we will persevere."
Protesters wearing typical farmer attire of woollen ponchos, brimmed hats and rubber boots to show their solidarity, marched in 15 columns toward the Plaza Bolivar, where the presidential palace and Congress are located.
There were also protests in Medellin, Cali and elsewhere across the nation.
Farmers have blocked roads, snarling city-bound traffic and piling pressure on Mr Santos three months before he must decide whether to run for a second term. The government's tough peace negotiations with Marxist FARC rebels are creating their own contentious national debate at the same time.
The clashes have led to at least one death.