Investigators have long used secretly installed surveillance software on phones and computers to monitor suspects' encrypted messaging services and other communications.
The Constitutional Court has now found that this is allowed only in cases where a conviction would lead to jail sentences of more than three years.
The judges said such surveillance represents a serious privacy intrusion and must therefore be limited to particularly serious crimes.
However, current rules will continue until the law is changed, the ruling said.
The court pointed to the "extraordinary reach" of telecoms surveillance in an age where all kinds of individual actions and interpersonal communications can be tracked digitally.
The data privacy group Digitalcourage had launched the case, supported by journalists and lawyers.
The group had urged more sweeping restrictions but nonetheless welcomed the ruling and vowed that "anyone who attacks our freedom must expect resistance".
The German Journalists' Association voiced disappointment, saying the court had "clearly prioritised criminal prosecution over informant protection".
"This makes it more difficult for us journalists to protect our sources," it said.
The German police union welcomed the decision to allow the continued use of the software in major cases.
"In times of terrorist threats, investigative authorities need effective tools for threat prevention and prosecution," said its chairman Rainer Wendt.
"With its ruling, the Federal Constitutional Court ensures that the rule of law can protect the population from the dangers of terrorism while simultaneously safeguarding their fundamental rights."
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