"Baaaaaaaaa bye, as we say it," Philippine Secretary of Foreign Affairs Teddy Locsin Jr wrote on Twitter on Friday morning.
The Philippines has said that the rubbish was falsely labelled as plastic recycling when it was sent to Manila in 2014, the BBC reported.
Canada has agreed to cover the full cost of its transfer and disposal.
A total of 69 containers were sent back in a cargo vessel that set sail from Subic Bay, north of Manila.
The roughly 1,500 tonnes of repatriated rubbish will be shipped to the Canadian city of Vancouver, arriving before the end of June, to be treated at a waste-to-energy facility there.
"This is a demonstration that we're going to comply with our international obligations to deal with waste that originates in Canada," Sean Fraser, Canada's parliamentary secretary to the environment minister, told the BBC on Thursday.
He said Canada had moved quickly in recent weeks to deal with the issue, which had dragged on for a number of years after the Philippines government made it "clear this is a very serious priority for them".
A growing number of countries across Southeast Asia are calling for Western nations to take back rubbish that has been sent to their shores, arguing that some of it was imported illegally.
( With inputs from IANS )