The sharply dressed 50-year old politician died in hospital after he was shot twice with sniper bullets.
Djindjic had only survived an attack on his life just three weeks ago.
He linked the attempt, when a lorry veered towards his car on a motorway outside Belgrade, to criminals whose business interests he has been threatening since taking office three years ago.
EU and world leaders condemned the killing last night amid fears it could severely set back Serbia’s slow climb towards democracy.
A spokesperson for the EU described the murder as barbaric. Foreign Relations Commissioner Chris Patten was due to meet Mr Djindjic today in Belgrade.
One of Mr Djindjic’s final acts was to pronounce the death of Yugoslavia and replace it with a loose union of Serbia and Monegro two weeks ago.
Reform-minded Mr Djindjic played a large part in the downfall of Yugoslav President Slobodan Milosevic, now on trial for genocide.
Jailed as a dissident student in the 1970s, frustrated as a popular protest leader in the 1990s, Mr Djindjic rebounded in 2000 in a lightning street uprising to become prime minister.
Mr Djindjic sought to crack down on the endemic corruption and organised crime in his country.
His premiership was tasked with tempering the breakaway ambitions of ethnic Albanians in the southern Serbian province of Kosovo and negotiating the dissolution of federal Yugoslavia into a loose union between the much-larger Serbia and the tiny, mountainous coastal republic of Montenegro.
He feuded with Milosevic’s successor, the more cautious former Yugoslav President Vojislav Kostunica, behind the scenes over the pace of reform, and the 18-party coalition they co-led split after Kostunica’s party left the coalition.
Mr Djindjic angered coalition partners with alleged attempts by associates to take control of mismanaged state enterprises in the chaos after the October 2000 uprising that ousted Milosevic.
Mr Djindjic was born in Samac, Bosnia, the son of a Yugoslav People’s Army officer.
He graduated from Belgrade University’s philosophy faculty but was imprisoned by Communist dictator Josip Broz Tito in 1974 for trying to organise an independent students’ group.
Upon release, he went to Germany to earn a philosophy doctorate.
He returned to Belgrade in 1989 and co-founded the Democratic Party, which he headed inside the (DOS) Democratic Opposition of Serbia reform alliance. His party, largest in DOS, took 12% of the vote in 1993 elections and admirers began referring to him as “Serbia’s Kennedy”.
It was then that he ditched his bohemian academic look, cut off his ponytail and turned to suits and ties.
In 1996, Mr Djindjic formed the Zajedno (Together) reform bloc with Vuk Draskovic and civil rights activist Vesna Pesic and it began mass protests after Milosevic annulled Socialist losses in municipal elections.
The three men led street marches and rallies that drew more than half a million people a day and went on for 88 straight days before Milosevic recognised opposition victories in key Serbian towns. Brooding bitterness with a decade of economic decay and international anonymity exploded in October 2000 when Milosevic refused to recognise election defeat to Kostunica.
Mr Djindjic, a fitness enthusiast is survived by his wife, Ruzica, a lawyer, and their two children.