"The work is not over. We want to normalise the bilateral relations" with Libya," said Foreign Minister Micheline Calmy-Rey.
Max Goeldi, who maintains he was the innocent victim of a diplomatic spat, told a news conference in the Swiss capital, Bern, that he was tired but happy to be reunited with his family.
"It is a moment that is full of emotion," said the 54-year-old, was this year sentenced to jail for visa offences and imprisoned for around four months before being freed on Thursday.
Goeldi and another Swiss businessman, who left the country in February, had been blocked from leaving Libyan territory after the brief arrest in Geneva of Hannibal Kadhafi and his pregnant wife in July 2008.
Kadhafi and his pregnant wife were detained by Swiss police after two of their domestic workers claimed they had been mistreated by the couple at a Geneva hotel.
Calmy-Rey acknowledged that the negotiations on the liberation of Goeldi had taken "much longer than expected".
Diplomatic ties further deteriorated when Tribune de Geneve published leaked police mugshots of Hannibal in September 2008.
A deal to settle the row was finally signed over the weekend under the mediation of Spain and Germany.