In the 5.30am incident, Memey Kandusan suffered severe burns on her face and abdomen and died several hours after admission to the Queen Elizabeth Hospital.
Penampang District Police Chief, DSP Ratan Kumar Singh, said the victim was approached by an unidentified man wearing a hat while she was having breakfast with two friends.
"No arrest has been made and the motive is being investigated," he said, adding the case is being investigated under Section 302 of the Penal Code.
He urged witnesses to come forward and assist police in the investigation.
Meanwhile, the eatery's 48-year-old manager, Mohd Hanifa, said the trio stayed above the shophouse, adding that there were only two female staff and one male staff on duty when the incident occurred.
He claimed that the floor of his premises turned white and that several cooking utensils were also damaged after the acid fell on them.
According to the victim's relative, Azlan Albab, the woman had seven siblings in Sandakan, adding that her mother also rushed to Penampang when she heard what happened to her daughter.
Also at the scene were Penampang District Police Crime Investigating Officer ASP Ho Siew Hoong and a forensic team from the police headquarters in Kepayan.