The daily Yeni Safak said its offices and those of Yeni Akit were attacked. No casualties were reported.
It said four masked assailants attacked the Yeni Safak building. Firefighters quickly extinguished the blaze.
Police have cordoned off the area around the building.
The two papers support the governing AK Party of President Recep Tayyip Erdogan.
The Yeni Akit offices are 20km (12 miles) away from the Yeni Safak building, and the night-time attacks happened almost at the same time, early on Thursday.
Windows in both buildings were shattered by the gunfire, Istanbul police said.
"Numerous spent bullet casings were also found at both scenes," the police added. They are now hunting the assailants.
So far no group has claimed it was behind the attacks.
Last September, pro-government protesters attacked the offices of the daily Hurriyet, accusing the paper of misquoting President Erdogan.

As part of the BBC's So I Can Breathe series, a week of stories exploring some of the different ways the world is seeking to reduce air pollution, people have been sharing their tips on how to improve the air around them.
For Phoebe, Joylen and Verity, from London, the answer is to stop cutting down trees.
Students at 50 London schools breathe air that exceeds legal pollution limits.
"Toxic air audits" have been announced by the mayor of London to combat the problem.
According to the US Forest Service, trees typically reduce urban air pollution by only up to 1%, but even this can have significant health benefits.
Areej and her mother also want to plant trees in urban areas of Damascus to improve air quality.
Wood-burning stoves are a cause of high indoor air pollution levels which have been linked to four million premature deaths annually, according to the World Health Organization.
Adboulie Sey thinks they should be banned from Gambia and solar energy promoted instead.
Africa's new breed of solar energy entrepreneurs
A tax on wood stoves is another solution, suggested by Karen Baines on Twitter.
Improving how we travel is a common desire.
Swapping driving for cycling can reduce the number of vehicles on the road emitting pollutants such as nitrogen dioxide.
Clare Rogers tweeted this picture of her and her daughter in Enfield.
Robert Singleton suggests a ban on diesel powered vehicles would go some way to reducing pollution.
Girl guides helping to clean Ghana's air pollution problem
Improved public transport is also proposed by Maria Innes in Buenos Aires, and echoed by Oscar Soria, in New York.
Mike Hall thinks government schemes to support people buying hybrid or electric cars is one way to encourage more environmentally friendly transport.
And Pablo Nieto Gonzalez in San Sebastian, Spain, wants emissions from ships to be cut.
A week of coverage by BBC News examining possible solutions to the problems caused by air pollution.

Dorset Police said officers had restrained the man, who was reported acting erratically in Poole on Tuesday.
The man suffered a medical episode while with the officers, who performed CPR while waiting for an ambulance.
He was taken to Poole Hospital but his condition deteriorated and he died on Wednesday morning, police said. His next of kin have been told.
Police have referred the death to the Independent Police Complaints Commission (IPCC).
A statement from the force said officers were called at 16:12 and 16:19 BST amid concern for the man's welfare.
The statement said: "When officers arrived, a man matching the description was found on The Avenue. He was restrained while officers assessed the situation.
"While with officers he suffered a medical emergency. The ambulance service was requested to attend and officers performed CPR while awaiting their arrival.
"The man was taken to Poole Hospital for further treatment. Sadly, his condition deteriorated and he died in hospital this morning."
Unidentified assailants have hurled petrol bombs and fired shots at the Istanbul offices of two staunchly pro-government Turkish newspapers, the papers and the police say.
[NEXT_CONCEPT]
From Ghana to Argentina and London, air pollution is a problem that people want to do something about.
[NEXT_CONCEPT]
A man who police had been called to help after he was seen wandering among traffic has died in hospital.