Public buses ran free of charge to the ceremony for the wartime military commander, who swallowed potassium cyanide last month during a court hearing broadcast live around the world.
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About 2,000 people filled the main concert hall where the memorial was held, while hundreds more crowed into the building's entry and hallways to watch on giant screens.
Praljak had a private funeral in Zagreb last week, according to media reports.
The 72-year-old took his life just seconds after appeal judges in The Hague upheld his 20-year jail sentence for war crimes and crimes against humanity during Bosnia's 1990s conflict.
'Theatre of the absurd'
The judges at the International Criminal Tribunal for the former Yugoslavia confirmed that Praljak and his five Bosnian Croat co-defendants were part of a "joint criminal enterprise" to ethnically cleanse Bosnian Muslims in the war.
But since Praljak's death, Croats have paid multiple tributes to the late general, laying flowers and lighting candles in town squares in Croatia and Bosnia.
Monday's commemoration, organised by the Croatian generals' association, was attended by at least one government minister in the EU member state, along with top officials of the ruling conservative HDZ party.
The event, which lasted around an hour, included music, recitals and speeches by Praljak's associates and friends from the military, politics and theatre.
"No one can compare to a great man like Slobodan," said Miroslav Tudjman, an MP with the HDZ and son of late Croatian nationalist president Franjo Tudjman.
Tudjman branded the UN court's verdict as a "degradation of international justice".
"It's a parody, a theatre of the absurd," said Tudjman, slamming "incompetent and irresponsible judges at the court in The Hague".
'Croatian martyr'
Zlatko Vitez, a well-known actor in Croatia, said that Praljak, who worked in film and theatre before joining the military, would be remembered as a "Croatian martyr".
The commemoration ended with a rendition of the Croatian national anthem led by a choir. The crowd, some of whom had travelled from Bosnia, stood up and joined the singing.
Before the ceremony, visitors queued up to sign two books of condolences.
Vjekoslav Balen, a 74-year-old pensioner in the queue, said Praljak was a "hero" who "took his own life for Croatia's wellbeing, for the future".
Later on Monday, a mass for Praljak was due to be held in a Zagreb church.
The appeals verdict for Praljak and his co-defendants was the last ruling from the ICTY before it shuts down at the end of the year.
Their convictions were upheld for crimes including murder, persecution and inhumane treatment.
Although allies against Serbs for most of Bosnia's 1992-1995 war, Croats and Muslims fought each other in 1993 and 1994.
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