The measures were supported by 410 MEPs with 205 against.
The Commission will now be requested to initiate new legislation with minimum standards for the protection farmed rabbits.
There are around 340 million rabbits slaughtered for meat in the EU every year and almost 100 per cent are raised in barren battery cages.
The mortality rate in the cages is extremely high, between 15-30 per cent a year - higher than for any other farmed animal. This is because rabbits are highly sensitive animals who are completely unsuited to these intensive and unnatural conditions.
Despite being the second most numerous farmed animal in the EU (after chickens), there are no legal minimum standards to protect them.
Investigations on more than 75 farms revealed the pain and suffering that caged rabbits endure, including rabbits left with open and infected wounds and countless dead rabbits left to rot in cages alongside living rabbits, and even cases of cannibalism due to the unnatural and stressful conditions.
Animal Equality and other groups had lobbied MEPs across Europe, sending more than 120,000 emails urging MEPs to support the long-fought initiative to protect farmed rabbits.
They included Vicky Ford, a UK ECR group member, who told this website she had received over 25,000 emails.
She said, "It's not clear which countries the senders come from. But the emails have helped to raise awareness of the issues with rabbit farming and the campaigners should be congratulated on their success in this."
The measures were supported by German GUE/NGL group MEP Stefan Eck.
Speaking after the vote in Strasbourg, he said Parliament had "rewritten history."
He added, "It proved that it can make a difference by listening to the voice of the people and act independently of the powerful industry lobbyists.
"By voting in favour of EU-specific legislation for farmed rabbits, the majority of the European Parliament has decided to take animal welfare and food safety seriously and to call on the Commission to close the existing legal loophole.
"MEPs have taken a huge step in the path to higher standards in animal welfare for hundreds of millions of animals. Now let's hope that the Commission will respond promptly to its mandate. I really hope they don't ignore our call."
GUE/NGL's Anja Hazekamp, a Dutch member of the Parliament's agriculture and rural development committee, said, "Farm rabbits are kept in atrocious conditions across the EU: they are locked up in cages which are far too small and cause injuries to their paws.
"On average, 25 per cent of farm rabbits do not survive these battery cages. For chickens, an EU-wide prohibition on battery cages is already in place. I am delighted that finally we are moving forward to getting legislation that will put an end to the suffering of farm rabbits as well."
Further reaction to the vote came from Toni Shephard, executive director of Animal Equality UK, who said, "History has been made. One of the cruellest farming practices ever invented, confining animals in tiny barren cages for their entire lives, could soon be obsolete in Europe.
"This is amazing progress for hundreds of millions of rabbits who currently endure extreme suffering in battery cages on European farms. Animal equality will keep working with European and national politicians until rabbit cages are confined to history."
Footage taken by Animal Equality investigators on rabbit farms in Spain and Italy was said to be instrumental in what Shephard hailed a "landmark decision."