Isaacson, CEO at the Aspen Institute and Steve Jobs' biographer, said the United States had developed the standards for reasonable search over the course of two centuries. He said smartphones should not be exempt from warrant searches.
He compared the idea of total online anonymity afforded by encryption to the Ring of Gyges, a mythical artifact cited by Plato that made the wearer invisible and capable of skirting justice.
"The question is, do you have a civil society and a rule of law if people can just put that on?" he said in an interview on CNBC's "Squawk Box." "It's not like our mobile phones should be separate from everything else in our lives."
"I don't believe that complete anonymity on everything you do helps make a better rule of law," he added.
Isaacson said the outcome was a positive one because the dispute would have been a "hard case," and hard cases make bad law.
"You don't want this whole thing to be settled on this San Bernardino case." he said. He noted that the dispute had brought a long-simmering conflict into the public eye.
Lawmakers and tech companies have long been at odds over the encryption being built into consumer devices.
Tech companies generally say encryption is necessary to protect their customers' privacy in a world besieged by data breaches. But national security and law enforcement officials worry it is creating a powerful tool for terrorists to communicate covertly and putting up high-tech roadblocks to investigations.