The accord follows frictions between the two countries over the case of a Tunisian rejected asylum seeker blamed for a truck rampage at a Berlin Christmas market that killed 12 people.
This agreement "will satisfy Tunisia and will satisfy Germany," Tunisian President Beji Caid Essebsi said at a joint press conference.
Merkel, on a two-day trip which also included a stop in Egypt, said Germany and Tunisia agreed on speedier repatriations for rejected asylum seekers and job training for Tunisians.
"We agreed that questions on identities (of Tunisian asylum seekers) from Germany will be answered within 30 days," she said.
Germany has previously said that Tunisian bureaucratic delays meant it could not expel the Tunisian suspect in the Berlin Christmas market attack, Anis Amri, even though his asylum application had been rejected six months earlier.
Speaking in Tunis, Merkel announced 250 million euros (USD 264 million) in development aid.
"The funds are for rural development, small and medium enterprises, but mainly for youths... Who especially need job training and employment opportunities," she said.
Merkel, who faces elections in September, is under pressure to reduce the number of asylum seekers coming to Germany, which has taken in more than one million migrants since 2015.
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