Federal prosecutors are treating the case in the city of Hanau as terrorism, with authorities saying indications point to an anti-foreigner motive.
In both places targeted on Wednesday night the clientele were reported to have been predominantly Kurdish.
The suspect was found dead at his home along with the body of his mother.
Police say the 43-year-old suspect killed himself. The Bild tabloid reports he was a German citizen with a firearms licence, and that ammunition and gun magazines were found in his car.
According to Bild, he expressed far-right views in a letter of confession and a video but this has not been confirmed officially.
What do we know about the attacks?
The shootings took place around 22:00 (21:00 GMT) on Wednesday, and the first target was the Midnight shisha bar in the city centre of Hanau. Witnesses reported hearing about a dozen gunshots.
The suspect then reportedly travelled in a dark car to the Kesselstadt neighbourhood and opened fire at the Arena Bar & Cafe.
Shisha bars are places where people gather to smoke a pipe known as shisha or hookah. Traditionally found in Middle Eastern and Asian countries they are also popular in many other parts of the world.
The shootings sparked a seven-hour manhunt, while officers searched for what they thought could have been more than one attacker. Witnesses led police to the suspect's home, near the scene of the second shooting, where he was found dead near his 72-year-old mother.
Hanau, in Hesse state, is a city of 100,000 residents about 25km (15 miles) east of Frankfurt. The attack happens amid growing concerns about far-right violence in Germany.
"What we know so far is that there is definitely a xenophobic motive. Whether there are claims of responsibility or documents, that's still being investigated," Hesse Interior Minister Peter Beuth said.
Can-Luca Frisenna, who works at a kiosk at the scene of one of the shootings, said his father and brother had been in the area when the attack took place.
"It's like being in a film, it's like a bad joke, that someone is playing a joke on us," he told Reuters news agency. "I can't grasp yet everything that has happened. My colleagues, all my colleagues, they are like my family - they can't understand it either."
Recent far-right attacks in Germany
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October 2019:
In Halle, an attacker kills two and tries to storm a synagogue, broadcasting the assault live online. He later admits a far-right, anti-Semitic motive for the attack
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June 2019:
Walter Lübcke, a pro-migrant politician, is shot in the head at close range and found dead in his garden. A suspect with far-right links later confesses to the murder
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July 2016:
An 18-year-old shoots dead nine people at a shopping mall in Munich before killing himself. Bavarian authorities later classify the attack as "politically motivated", saying the teen had "radical right-wing and racist views"
What has the reaction been?
Hanau Mayor Claus Kaminsky told Bild it had been a "terrible night", adding: "You could not imagine a worse night. It will of course keep us busy for a long, long time and remain a sad memory. I'm deeply moved."
Katja Leikert, who represents Hanau in the German parliament, the Bundestag, said: "Hopefully the injured recover swiftly. It is a horrific scenario for us all."
On Twitter, Germany's government spokesman Steffen Seibert said: "My thoughts are with the people in Hanau this morning, where an appalling crime was committed."
Gun laws in Germany are among the most stringent in the world, and were tightened further in recent years after other mass shootings. BBC