“I recognize your concerns,” Stoltenberg told a joint news conference with Turkish Foreign Minister Mevlut Cavusoglu in Istanbul.
He said Finland and Sweden were keen to work closer with Turkey to fight “terrorism”.
“It’s also in their interest,” he said.
“It’s time to welcome Finland and Sweden as full members of NATO. Their accession will make our alliance stronger and our people safer.”
Both countries dropped decades of military non-alignment and scrambled to become NATO members in May, Â after Russia invaded Ukraine.
But Turkish President Recep Tayyip Erdogan threatened to block their bids, seeking concessions.
In June, Turkey, Sweden and Finland struck a deal which included provisions on extraditions and sharing information.
“Finland and Sweden have delivered on their agreement to Turkey,” Stoltenberg said.
“They have become a strong partners in our joint fight against terrorism in all its forms and manifestations,” he added.
“And they are clearly committed to long-term engagement with Turkey to address your security concerns.”
To date, all but Turkey and Hungary of the 30 NATO member states have ratified the accession of Sweden and Finland.
New members to the alliance require unanimous approval.
Cavusoglu said Stockholm took some steps including the removal of restrictions standing in the way of arms sales to Turkey but added “it’s not possible to say” the July agreement was fully implemented.
“We don’t intend to harm NATO or block its enlargement … we want to see concrete steps,” he said.
Ankara is “more hopeful” that Sweden’s new government will address Turkey’s concerns, Cavusoglu added.
Sweden’s new Prime Minister Ulf Kristersson would visit Ankara on Tuesday for further talks, the foreign minister said.
NATO accession is a priority for Sweden’s new right-wing government.
Stoltenberg, who is due to meet with Erdogan on Friday, said it was important to finalize the membership bids to send a “clear message to Russia”.
“In these dangerous times it is even more important to finalize their accession to prevent any misunderstanding or miscalculation by Moscow and to send a clear message to Russia that NATO’s door remains open,” he said.
“And it is only for allies to decide on NATO membership, nobody else.”