About 1500 protesters tried to march to the Hotel Indonesia traffic circle, a key city landmark, after Friday prayers.
Authorities stopped many of them and also blocked streets leading to the presidential palace, where many protests often end up.
More than 6000 police and soldiers were deployed there.
Protesters, many wearing yellow university jackets, voiced their frustration over living costs, which have risen as a result of higher fuel costs since the US launched its war against Iran.
Indonesia's rupiah currency has come under pressure, hitting a historic low of 18,000 rupiah to the US dollar earlier in June.
Protesters outlined five key demands, including cuts to what they called wasteful state spending, lower prices for fuel and staple goods, and a halt to major government programs such as a free nutritious meal initiative and a plan to revitalise rural areas.
The free meals program, costing about 268 trillion rupiah ($A21 billion) for 2026 alone, is aimed at alleviating poverty and malnutrition but Prabowo recently fired the head of the program amid a massive graft probe.
They also called for an end to what they described as the increasing role of the military in civilian affairs, something they view as a threat to the young democracy.
"The government is in denial about the current situation," said Yatalathof Ma'shum Imawan, who chairs the student organisation that organised the rally.
"We urge Prabowo to have the courage to acknowledge his mistake and stop denying it."
Friday's demonstration marks one of the largest student mobilisations since nationwide protests erupted in August 2025, when thousands took to the streets and clashes with security forces left at least 13 people dead.
Similar protests were also held in West Java's Bandung city and in Pontianak, a city on Borneo island.
