Lawmakers gave near-unanimous approval to the bill, which represents a major step for LBGT rights on the island, which only legalised divorce in 2011 and where abortion is outlawed.
Malta, the EU's smallest nation, becomes the bloc's 15th country to legalise same-sex unions.
The vote was one of Prime Minister Joseph Muscat's first actions following his election victory last month.
"It's a historic vote. This shows that our democracy and society have reached a level of maturity and we can now say that we are all equal," he said after the text was passed.
The influential Catholic church was solidly opposed to the bill but gay rights activists on Wednesday hailed the result, rallying in downtown Valetta under the banner: "We've made history".
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