Yıldırım said at a press statement with Merkel that Yücel's case should not be a major problem for the two allies.
Mr Yucel, who has German and Turkish citizenship, was arrested in Istanbul on February 14 past year on terrorism and propaganda charges which he denies.
Relations have recently started to recover from their deep crisis after Turkey released several German citizens.
"I can assure you there were no agreements, no quid pro quo and no - as some people call it - deal in this case", Gabriel said.
The issue also came up at a meeting on Thursday between Turkey's prime minister, Binali Yildirim, and German Chancellor Angela Merkel.
Deniz Yucel was detained last February on suspicion of spreading propaganda in support of a terrorist organisation and inciting violence. "Deniz Yucel is free", German Justice Minister Heiko Maas said in a tweet.
Turkey's state-run Anadolu news agency said the court had accepted an indictment seeking up to 18 years in jail for Yucel but had also opted to free him ahead of trial. He denies the accusations. They include Ahmet Altan, the former editor-in-chief of Taraf newspaper, his brother, journalist and academic Mehmet Altan, and prominent journalist Nazli Ilicak.
Turkey, the USA, and the European Union list the PKK as an armed terrorist organization, which has been raging an armed conflict against the Turkish state since the mid-1980s.
She was held for over half a year on charges of membership of the Marxist-Leninist Communist Party (MLKP), which is banned in Turkey as a terror organisation.