About 150 people were wounded in the attack that took place on August 21, 2004, police and party officials said.
Badar Azizuddin, an Awami League supporter who was injured in the attack, filed the case, also accusing Lutfuzzaman Babar, a former junior home minister, and Muddabir Hossain, then police chief.
The court, on Tuesday, asked police to complete the investigations and submit a report as soon as possible.
Babar was himself detained by security forces last week in an anti-corruption sweep, and is being held in jail prior to trial.
Police did not probe the 2004 grenade assault, the country's worst attack on a political rally, during the rule of Zia, which ended last October.
"Government actions after the incident proved that the then prime minister and her colleagues engaged professional killers to eliminate opposition leader Sheikh Hasina once [and] for all," a court official quoted from the case petition.
Hasina and Zia alternated as prime ministers of the impoverished south Asian country for 15 years from 1991 but remained bitter foes, without speaking to each other for more than a decade.
Hasina herself faces charges of murder linked to political violence in the capital, following Zia's exit from power, which led to the imposition of emergency and ban on political activity by the interim authority.
The authority also cancelled an election planned for January 22.
Officials said the military-backed government is targeting both the ex-premiers in the anti-corruption drive as their family members and relatives have been detained on charges of graft, extortion and abuse of power.
Separately, the interim administration has barred loan defaulters from serving on the committees of business groups, which are seen as a stepping stone to politics.
Mohammad Ali, currently senior vice-president of the Federation of Bangladesh Chambers of Commerce and Industry [FBCCI], is among the top loan defaulters, central bank officials said. He is viewed as a frontrunner for president in the next FBCCI election.
Many top trade body leaders also keep close links with major political parties or their leaders, giving them money in return for business favours, officials said.
Army-led security forces have detained two former FBCCI chiefs - Salman F Rahman and Abdul Awal Mintoo - for allegedly bribing the parties of Hasina and Zia.
Mintoo was detained in the latest anti-corruption sweep last week, while Salman was arrested in March.