Prosecutors in Geneva said that the decision was taken on this year, and that they had only opted to make it public as a result of street protests in Pakistan.
They declined to comment in detail, but the Swiss news portal 20minutes.ch published photographs of anti-Zardari protestors burning Switzerland's flag at a rally in Pakistan.
Zardari and Bhutto were alleged to have siphoned $12 million in state cash in the 1990s, when he was a government minister and she was premier.
Bhutto lost office in 1996, and a year later Pakistan made a formal request for Swiss legal help in a probe of the couple and Bhutto's mother Nusrat Bhutto.
Bhutto went into self-imposed exile in the United Arab Emirates in 1997, returning in 2007, only to be assassinated in a bomb attack on an election rally the same year.
Weeks before Bhutto was killed, Pakistan had withdrawn its request for help from the Swiss, and Geneva investigators formally closed their side of the probe in 2008.
Zardari, meanwhile, was arrested in Pakistan on graft charges after his wife's government fell, before being freed in 2004, going into exile in the United Arab Emirates, then returning after Bhutto's death.
He was elected president in 2008.
In November 2012, however, Pakistan's government renewed its request for Swiss legal assistance after being ordered to do so by its own supreme court.
Geneva prosecutors underlined that no new evidence had emerged since the case was dropped in 2008, meaning they could not reopen the investigation.
In addition, the fact that the alleged offences took place more than 15 years ago meant that the statute of limitations had expired, they said.
They also complained about mixed messages from Pakistan.
Just a month after filing the renewed request, Pakistan sent them a letter stating that the call for a revived probe was linked to domestic politics and that there was no need to heed it.
That amounted to abuse of the legal system, prosecutors said.