According to the Chicago Police District, the weekend had begun relatively quiet but violence spiked on the last day with 31 shots between 6 a.m. Monday and 3 a.m. Tuesday.
Nine of the 13 fatalities were shot during this period, according to a Chicago Tribune report.
CPD police chief Eddie Johnson blamed the bloody incidents to impoverished neighborhoods where "people without hope do these kinds of things.
"Impoverished neighborhoods, people without hope do these kinds of things. You show me a man that doesn't have hope, I'll show you one that's willing to pick up a gun and do anything with it," said Johnson as quoted by the report.
Police said most of the killings have occurred in Chicago's southern and western neighborhoods, where 75 community organizations hosted block parties, concerts and other pop-up events over the holiday weekend.
Among those who were fatally shot were a pregnant woman and a pastor.
The Labor Day weekend was the deadliest of the three holiday weekends this summer -- the Memorial Day weekend saw 69 shot, six of them fatally, while the Fourth of July weekend recorded 66 shot, five of them fatal.