"We are in a repeated game where a political dysfunction is going to be an issue for markets," he said, adding that the global and U.S. economies are not growing fast enough to overcome the headwinds from Washington.
The U.S. economy "is able to endogenously heal and grow faster if only these headwinds were to get out of the way," El-Erian said. He expects growth of a "solid 2.5 percent."
The problem with the deal is that the fundamental issues were not addressed, he said, and the same concerns will resurface in a few months. An agreement was reached not because of "some great compromise" but because both parties were exhausted—after great damage was done, he added.
(Read more: This is what theshutdown really cost you)
That setback will cause the Federal Reserve to postpone tapering at least until Janet Yellen becomes a head of the Fed, El-Erian said. The Fed will be "more accommodative for longer," he said, buying more insurance ahead of yet another round of political brinkmanship.
"But this notion of taper is less probable now given what has happened," El-Erian said.