The budget Irish airline said it would take the €210m deal to European competition authorities.
Lufthansa plans to use Air Berlin planes to expand its Eurowings budget airline business.
Air Berlin filed for bankruptcy in August after its main shareholder, Etihad, said it would not give further financial support.
Flights continued after a transitional loan of €150m from the German government.
Germany's second-largest carrier has since been negotiating with potential buyers for parts of its business.
Lufthansa has agreed to buy Air Berlin's Austrian leisure travel airline Niki, its LG Walter regional airline and 20 additional aircraft.
Ryanair previously described the negotiations as a "stitch-up" intended to strengthen Lufthansa.
"We will be referring the matter to the EU competition authority in due course," a Ryanair spokesman.
Andreas Mundt, head of Germany's cartel office, said the European Commission would take a close look at the deal and that German authorities would follow the process closely.
Lufthansa chief executive Carsten Spohr said earlier he expected the Air Berlin deal to receive European Union approval by the end of the year.
Shares in Lufthansa rose 2.8% in Frankfurt.
Air Berlin, which accumulated debt for almost a decade, reported a record loss of €782m (£713m) for last year.