As outlined in the new proposal, member states will have to provide assistance to persons and boats in distress, follow the principles of 'non-refoulement' - the returning of persecuted individuals to their country of origin - and identify intercepted migrants.
In addition states are forbidden to 'push back' vessels attempting to enter the EU, and criminal sanctions on those who rescue migrants who are entering the EU are to be lifted.
Carlos Coelho, parliament's rapporteur on the dossier, said, "The agreement reached today which lays down rules for the surveillance of external sea borders is a success story.
"We are happy with this outcome because saving human lives is something that cannot be questioned, especially by any vessel that has the ability to do so.
"We are happy with this outcome because saving human lives is something that cannot be questioned" - Carlos Coelho
The Portuguese MEP explained, "These new rules will contribute to a more effective surveillance of our external borders and will fight against all forms of cross-border criminality.
"This agreement safeguards that those who are intercepted or rescued, in particular those in need of international protection, victims of trafficking, unaccompanied minors and other vulnerable persons, are identified and receive appropriate help.
"I believe that the EU was able for the challenge, and within our legislative powers we stood up for what we believe in: a Europe of values," concluded Coelho.
Home affairs commissioner Cecilia Malmström welcomed the outcome, saying, "Today's vote is an important step towards enhancing the effects of sea border surveillance operations and to improve coordination in search and rescue situations that may arise during such operations.
"We have witnessed too many tragic losses of lives in the Mediterranean recently: having clear binding rules on interception, search and rescue and disembarkation will help preventing such tragedies in the future.
"The new rules will ensure the effective and proper functioning of current and future Frontex-coordinated sea operations, contributing to protecting and saving migrants' lives.
The Swedish official continued, "The new regulation strengthens the protection of fundamental rights, including the application of the principle of non-refoulement in case of disembarkation in a third country.
"It also sets out clear procedures to be followed by border guards when facing a rescue situation during a border surveillance operation, in particular to assess the emergency situations of migrant boats."
Also speaking after the vote, S&D deputy Sylvie Guillaume, said, "It is no secret that although international rules set out a duty to render assistance to persons in distress at sea, the reality on the ground is different. It was therefore time for the EU to make some concrete contribution towards preventing the deaths of migrants attempting to reach Europe.
Clearly, this new regulation will not transform Frontex into a humanitarian agency, but within its mandate, it will provide the EU Agency with clear and binding rules on sea operations.
However, she added, "The success or failure of this system will now depend on the way it is applied and its implementation must be closely monitored. But let us not fool ourselves, Frontex and border surveillance cannot be the alpha and omega of the European migration policy.
"As long as the EU and its member states prefer unilateral and short-term responses, and continue to be obsessed with security rather than adopt a global, responsible and long-term approach to migration, it is to be expected that migrants will keep resorting to ever more dangerous routes," she concluded.
Although Greens migration policy spokesperson Ska Keller was less optimistic about the new agreement, saying, "The protection of refugees at sea is an inviolable principle that the EU should uphold.
"The protection of refugees at sea is an inviolable principle that the EU should uphold" - Ska Keller
"While the rules adopted today include some clear improvements on the current situation, concerns remain that Frontex sea operations will still be able to repel refugee boats without properly assessing whether refugees on intercepted boats need protection in the EU.
She added, "This would be at odds with a European Court of Human Rights (ECHR) ruling on the duty to protect refugees at sea."
The German MEP continued, "The new rules include binding provisions on search and rescue. Importantly, the fundamental principle of non-refoulement of people who face persecution is explicitly detailed in the new rules, following Green insistence.
"Frontex will also have a duty to include medical assistance, translation and legal advice in planning its operations. However," she added, "concerns remain".
"As a translator does not have to be on board the FRONTEX boat and only available to be called if necessary, there is no guarantee that refugees can make it clear that they need protection in the EU.
"Refugees will also have no means to contest an attempt to send boats back. This is in spite of the fact that the ECHR judgement made clear that refugees must be given immediate legal means to appeal any such decision. This is unacceptable for the Greens," she said.