The Tuesday evening attack on Kramatorsk wounded 61 other people, Ukraine's national police said, as strikes rained across the country late on Tuesday and early Wednesday.
The ongoing attacks came as Russian President Vladimir Putin met with military staff in the Kremlin on Tuesday, trying to repair the damage to his authority from a mutiny led by Wagner private army chief Yevgeny Prigozhin.
He flew to the Caspian city of Derbent, in the mostly Muslim region of Dagestan, on the Islamic holiday of Eid al-Adha on Wednesday. Putin visited an ancient citadel and a historic mosque, met with officials, and walked to cheering crowds next to a fountain, talking to people and shaking hands — rare behaviour for the secretive and reserved Russian leader.
Prigozhin went into exile in neighbouring Belarus on Tuesday, according to Belarus President Alexander Lukashenko, after Russia said he wouldn't face charges for the revolt. Prigozhin's whereabouts could not be independently confirmed.
Lukashenko has said his country would allow Wagner to set up a temporary camp in Belarus, but it remained unclear how many mercenaries would move there.
Ukrainian President Volodymyr Zelenskyy played down concerns that Wagner would pose a threat from Belarus.
He said the group's mercenaries probably wouldn't go there in significant numbers, and added that Ukraine's military believes security along the Belarusian border will remain "unchanged and controllable".
US President Joe Biden said on Wednesday the unrest had weakened Putin, though he added that it's "hard to tell" to what extent.
"He's clearly losing the war in (Ukraine)," Biden said of Putin. "He's losing the war at home and he has become a bit of a pariah around the world."
In Kramatorsk, two 14-year-old sisters died in the attack, the city council's educational department said. "Russian missiles stopped the beating of the hearts of two angels," it said in a Telegram post.
The other dead teenager was 17, according to Prosecutor General Andrii Kostin.
The attack also damaged 18 multi-story buildings, 65 houses, five schools, two kindergartens, a shopping centre, an administrative building and a recreational building, regional governor Pavlo Kyrylenko said.
Rescuers were still searching the rubble for bodies and more survivors in a city where last year, about six weeks after the start of war, 52 civilians were killed in a Russian missile strike on a train station.
Kramatorsk is a frontline city that houses the Ukrainian army's regional headquarters. The pizza restaurant was frequented by journalists, aid workers and soldiers, as well as local residents.
The Security Service of Ukraine said the man it detained, an employee of a gas transportation company, is suspected of filming the restaurant for the Russians and informing them about its popularity.
The Russian Defence Ministry said its forces hit a facility used by Ukrainian army officers in Kramatorsk but did not mention the pizza restaurant that was struck.
Kramatorsk is in Donetsk, one of four Ukrainian provinces that Russia annexed last September but does not fully control. In 2014, Russia also annexed Ukraine's Crimea.