With the freeing of the two journalists, two others of the seven arrested in January remain in police custody over the video that went viral on social media in December, the Union of Journalists of South Sudan (UJOSS) said.
The journalists - staff at the state-run South Sudan Broadcasting Corporation - were arrested by agents from the National Security Service as part of an investigation into the source of the video purportedly showing the nation's president soiling himself.
In the footage, Kiir, dressed in his trademark black hat and a grey outfit at what is described as a road commissioning ceremony, is seen with a damp patch on his left trouser leg.
"We are still calling on the government to release the two (journalists) who are still behind bars," UJOSS president Patrick Oyet told AFP.
Oyet urged the government to present the duo in court if they have broken any law, adding that the probe had dragged on for months.
"The law says you should carry out investigations and produce somebody in the court within 24 hours."
"If there is no case they should be released," he said.
In January, the New York-based Committee to Protect Journalists called for the unconditional release of the journalists and for state authorities to "ensure that they can work without further intimidation or threat of arrest."
The arrests match "a pattern of security personnel resorting to arbitrary detention whenever officials deem coverage unfavorable", said CPJ's sub-Saharan Africa representative, Muthoki Mumo.
Kiir, 71, oversaw the birth of South Sudan as an independent nation after it broke free from Sudan in July 2011.
But the world's youngest country has lurched from crisis to crisis since then, enduring brutal conflict, political turmoil, natural disasters and hunger.
South Sudan ranks 128th out of 180 countries on the Reporters Without Borders (RSF) press freedom index.
According to the media watchdog, freedom of the press is "extremely precarious" in the landlocked nation, "where journalists work under constant threat and intimidation, and where censorship is ever-present."