The body of 30-year-old Viktoria Marinova was found on Saturday close to a jogging path by the Danube, Ruse prosecutor Georgy Georgiev said.
It is not known if Marinova's murder is linked to her journalism work.
Marinova was an administrative director of Ruse's small private TVN television and had recently launched a new current events talk show called "Detector".
Prosecutors confirmed she had also been raped and her personal items had been stolen.
The pair were briefly detained by police, drawing condemnation from Reporters Without Borders (RSF). "I urge them to swiftly identify and bring to justice those responsible and to clearly determine whether this attack was linked to her work", he said. "It was meant to serve as an example, something like a warning".
Bulgarian prime minister Boyko Borissov said: "It's only a matter of time before the murderer will be revealed".
Among the most high-profile recent cases were Malta's anti-corruption blogger Daphne Caruana Galizia who died in a vehicle bombing outside her home in October 2017, and top Slovak reporter Jan Kuciak who was shot dead with his fiancee at their home in February.
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A reporter from TVN told AFP, "We are in shock".
As The Guardian noted, Bulgaria was ranked 111 of 180 countries in this year's Reporters Without Borders world press freedom index. Swedish freelance journalist Kim Wall was murdered in a gruesome case in Denmark past year by Danish inventor Peter Madsen.
She recently reported on an investigation by a group of Bulgarian journalists into companies involved in EU-funded infrastructure projects administered by local authorities. "Her new programme doesn't seem to offer any motive to kill her", said Tihomir Bezlov, of the Center for the Study of Democracy (CSD) in Sofia.
Caruana Galizia had investigated government corruption, including in sales of European Union passports to wealthy foreigners.
"With enormous pain and insurmountable grief the team of TVN television is experiencing the loss of our beloved colleague, Victoria Marinova", TVN said in a statement.
He also called on the Bulgarian government to do more about protecting the safety of journalists working in the country generally.
Bulgarian media reported Monday that the park where Marinova was killed is adjacent to a psychiatric facility and authorities were investigating whether a patient could have been Marinova's attacker. He accused the mainstream media of leading a "massive smear campaign" against him.
She says "whatever results the investigation (into Marinova's death) shows, people won't believe them".
A candlelight vigil in Marinova's memory is organised for Monday evening in Sofia.