City's Bernardo Silva and Mateo Kovacic both misfired in the shootout to put Madrid in the driving seat
The decision, which Bolt's manager Ricky Simms confirmed to Reuters, came a day after the Jamaican sprinter ran the fastest indoor 100m ever, clocking 9.98 seconds in Warsaw.
"His coach Glen Mills ... feels it is now time to shut it down while he is healthy and injury free with a view on his preparations for the 2015 season," Zurich organisers said in a news release.
Bolt had delayed the start of his season to recover from minor foot surgery and a hamstring injury and had run only three races this season.