"Based on evidence recovered during today's investigations, SPD believes a lone suspect is responsible for the murders in Roosevelt and First Hill," police said in the blog post. "Still, neighbors should expect to see a heightened police presence as detectives work to confirm links between the two tragic incidents."
Roosevelt High School, which is near the cafe, was put on lockdown while police armed with rifles continued to search the area.
Two other nearby schools, Greenwood Elementary School and Eckstein Middle School, were put on a modified lockdown, the Seattle Post-Intelligencer reported.
No one answered the phone at Cafe Racer. A recorded message urged callers to "remember to come visit us, where we keep safety third."
"We've had two tragic shootings today that have shaken this city," Seattle Mayor Mike McGinn told reporters.
He said he has asked police to find ways to end the gun violence.
"It's their highest priority to identify the strategies we need to employ to try to bring an end to this wave of gun violence that this city is seeing," he said.
ABC News' Kevin Dolak, Josh Haskell, John Capell and ABC News Radio contributed to this report.