Siddiqui died on 14 April 1994 due to cardiac arrest after a brief illness in Karachi. He was buried in the Karachi University Graveyard. Despite his death, the academic and research institutes that he founded during more than 65 years of his research career are still contributing to the international level research in natural products chemistry.
As a person of multiple talents, Siddiqui was also a refined poet, musician, and a painter. In August 1924, he held his first international exhibition of paintings in Frankfurt. Later in 1927, his works of art were exhibited at the Uzielli Gallery, Frankfurt. During his stay in Germany, he also translated Rainer Maria Rilkes poetry into Urdu, which was published in the journal of Jamia Millia Islamia. Though, his passion for arts was superseded by the enthusiasm in scientific research, he continued to patronise arts and culture. In 1966, he was at the forefront for setting up the Central Institute of Arts and Crafts in Karachi. He also compiled a selection of poetry of Mir Taqi Mir into Intekhab-e-Meer'. In 1983, he published a portfolio collection of charcoal drawings from 1920 to 1950s.
On 14 April 1999, the Pakistan Post, as part of its Scientists of Pakistan series, issued a commemorative stamp to honour the contributions and services of Siddiqui. In the same year, the street leading to PCSIR Laboratories Complex in Karachi was named as Shahrah-e-Dr. Salim-uz-Zaman Siddiqui. Siddiqui was also remembered by his students and colleagues, many of whom continued to dedicate their international research and publications to his memory. In 2002, a research article was published in the journal Tetrahedron in which, authors Faizi and Naz dedicated their break-through research to the memory of Siddiqui, their mentor.