According to an e-mail from the border section of the German federal police headquarters, the restrictions only apply when arriving from Austria, Denmark, France, Italy, Luxembourg, Spain, Switzerland or from outside Schengen.
However, the TIMATIC database, used by airlines, states the restrictions apply everywhere. Since IATA gets their info from the federal police headquarters (at least in part), this confuses me and I am in fact seeking clarification on this as we speak.
Passengers are not allowed to enter Germany.
This does not apply to passengers with evidence that their travel is to perform
a professional activity, e.g., commuters, diplomats,
nursing staff, food industry personnel, specialists
So in practice, the check-in staff in Tallinn will require evidence of your business activity.