From 1947 to 1956, Johnston taught at Stanford University. While there, he was named to the editorial board of the Journal of the American Chemical Society. In the early 1950s, Johnston furthered the air pollution work of Arie Jan Haagen-Smit by showing that free-radical reactions underlay the photochemical process leading to smog. Throughout his career, much of Johnston's work involved understanding the kinetics of nitrogen oxides. He returned to Caltech as a faculty member for a year in 1956.
From 1957 until his retirement in 1991, Johnston was a professor at the University of California, Berkeley. From 1966 to 1970, Johnston was the dean of Berkeley's college of chemistry. Johnston mentored undergraduate and graduate students, including future Nobel Prize winner Dudley R. Herschbach and future National Medal of Science winner Susan Solomon. He also made large contributions to the theory of elementary chemical reactions. He wrote a popular textbook on reaction rate theory.
Johnston became best known for his work related to ozone. In a 1971 paper, he posited that pollution from supersonic aircraft in the stratosphere could deplete the ozone layer. Because it suggested for the first time that human activity could impact the integrity of the environment, Johnston's ozone research received some criticism and resistance. However, two environmental regulatory programs were formed as a result of his findings – the Climatic Impact Assessment Program (CIAP) and the Stratosphere Protection Program.