Johnson said additional officers had been deployed to prevent retaliatory shootings, leading to the arrests of 46 people on firearms charges. However, anti-violence protesters recently shut down freeways in Chicago to voice their outrage.
The spate of violence erupted just after midnight, and two people were killed and 28 others were hurt in shootings before 3 a.m.
There were six shootings in the city on Friday evening, though none were fatal, and a further 15 people were shot on Saturday, one of whom died.
Waller said numerous incidents were targeted, gang-related shootings, and in some cases, suspects were using larger summer crowds as cover.
Chicago has done much to combat its high shooting and murder rates in recent years, with Mr Waller claiming shootings are down 30% from 2017, and murders are down 25%. Later Sunday morning, Jahnae Patterson, 17, was killed and five other people wounded, including an 11-year-old boy in a shooting in the 1300-block of South Millard Avenue.
In some of the incidents, gunmen had shot into large crowds in a few of the districts. "We will not, I promise you that we will not be defeated".
The youngest survivor is an 11-year-old shot in the leg.
Three or more victims have been wounded in seven of Sunday's shooting incidents, including a single shooting in the South Side Gresham neighborhood left eight people wounded, including four teenage girls. In that incident, three people were standing in front of a residence when a shooter exited a auto and opened fire, according to officials.
Forty-four people were shot across the Midwestern US city of Chicago Sunday, US media reported, with five killed in a wave of violence police branded "totally unacceptable".
The spike in shootings overwhelmed paramedics and hospitals.
Chicago's gun violence has drawn widespread attention, including from Mr Trump and his lawyer, Mr Giuliani, who blamed the problem on Chicago's long-time "Democratic rule" in a series of tweets on Sunday and Monday. "I hear people holding us accountable all the time", Johnson said.
The police chief emphasized an oft-repeated criticism by city officials that repeat gun offenders receive sentences that are too short and are able to quickly return to the streets to commit more crimes - believing they will not face serious consequences. While we shouldn't condone the use of tactics which close down infrastructure in the name of free speech, it's clear that the residents of the city have plenty to be upset about.