Spain's main opposition party, the socialist PSOE, abstained from the vote which has been labelled a blow to Spain's idea of universal justice.
The move could see the shelving of as many as a dozen high profile Spanish-led international cases involving genocide, torture and war crimes.
These include cases looking at alleged Chinese genocide in Tibet in the 1980s and 1990s and torture of prisoners at the US military prison of Guantanamo Bay in Cuba.
It is part of changes to the legal system which will mean the country's courts can only investigate crimes either involving Spaniards or taking place on Spanish soil.
But a spokesperson for the PSOE on Thursday slammed the vote saying: "It's as if the the Chinese regime were imposing the order of the day."
"This news is sad because Spain has been something of a beacon in the fight for human rights with its investigations into human rights abuses in countries like Chile and Argentina," Ignacio Jovtis of Amnesty International told The Local in January.
"Once again Spain is putting its political and economic agendas above human rights," he added.
The Spanish Government had defended the changing, saying the changes are in line with its ratification of the statute of the International Criminal Court.
Most of the cases affected, however, involve countries which have not ratified that statute, including the US and China, El País newspaper pointed out.
Spanish legal investigations into torture at Guantanamo Bay and genocide in Tibet have caused serious diplomatic tension with the US and China.
Last November, Spain's National Court authorized the arrest of former Chinese President Jiang Zemin and four of his officials, a decision which angered the Asian superpower.
Spain's ambassador in Beijing was called in by the Chinese Government and Spain threatened with economic reprisals, the ambassador said.
The court's public prosecutor is now looking to have the arrest order overturned citing procedural issues.
The new law is expected to take force in March.