The ringleaders of the "Bali Nine" heroin smuggling operation, Chan and Sukumaran had asked the State Administrative Court to overturn its earlier decision, in February, that presidential decrees fall outside its jurisdiction.
But the three judges ruled yesterday that the "refusal of clemency is not in [the court's] authority ... That is the President's decision".
Last December, claiming that the country was facing a "drug emergency", Widodo announced that none of the 64 drug criminals then on death row would have their sentences commuted to life imprisonment. Six of those, including five foreigners, were executed in January.
The Australians, widely recognised to have rehabilitated themselves during a decade in jail, argued that the President - who is under domestic pressure to take a hard line on drugs - is duty-bound to consider each plea for clemency in detail and individually.
One of their lawyers, Todung Mulya Lubis, a prominent human rights advocate, said the fight was not over for the pair, who are being held in semi-isolation on the Central Java prison island of Nusakambangan.
"We have anticipated that the court would be very legalistic," he tweeted. "The court failed to understand the miscarriage of justice. The struggle to find justice continues. We lost our fight in the court. We have not lost our fight in finding justice."
Last week, Lubis said the legal team was "still trying to think outside the box".
If the latest appeal was rejected, Lubis said, "we will have to find our way ... to launch another legal action".
But it is doubtful whether there are any further legal avenues to pursue. After presenting their case to the Administrative Court last week, another of the pair's lawyers, Leonard Arpan, said: "We did our best."
Indonesia's Supreme Court has yet to rule on judicial review applications from two of the other eight death row prisoners, Frenchman Serge Areski Atlaoui and Ghanaian Martin Anderson. However, decisions are expected as early as this week.
The court has already rejected similar applications by Nigerian Raheem Agbaji Salami, Filipina Mary Jane Fiesta Veloso, the only woman in the group, and the one Indonesian, Zainal Abidin.
Salami is also planning an appeal in the Administrative Court. But all the legal hearings are expected to be fast-tracked. Veloso's request for judicial review was rejected within days, while the process normally takes up to three months.
Another of the eight, Brazilian Rodrigo Gularte, has been deemed mentally fit to be executed, despite being diagnosed with schizophrenia.
Brigid Delaney, co-founder of the Australian-based Mercy Campaign, yesterday tweeted: "No words ... Just such a heavy feeling of sadness."
Chan and Sukumaran were condemned to death in 2006, after being convicted of trying to leave Bali with 3.8kg of heroin, to import into Australia.
Speculation that Indonesia might delay the executions until after it has hosted the Asia-Africa Summit in the city of Bandung on April 19-23 - to which more than 100 national leaders have been invited - has been dismissed by Attorney-General Prasetyo.
What next for the two Australians?
•Lawyers for Andrew Chan and Myuran Sukumaran have said they will try to mount another legal challenge, but it is unclear whether any further avenues remain to
be explored.
•Indonesia has said the pair will be executed at the same time as eight other death row prisoners, including seven other
foreigners.
•The executions will not take place until all 10 convicted drug criminals have exhausted all their legal appeals. But that could happen within a matter of weeks, or even sooner.
•Indonesian law requires that all death row prisoners be given 72 hours' notice of their date of execution.
•All 10 will face a firing squad on the prison island of Nusakambangan.
