A ceremony was due to be held at Kandahar airfield to mark the formal end of combat operations, although hundreds of troops will stay on in a training role.
Canadian soldiers first deployed to Afghanistan in early 2002, several months after a US-led invasion of the country to oust the Taliban in the wake of the September 11 attacks.
In recent weeks they have been completing their final patrols, packing up dusty outposts and gathering at the giant Kandahar airfield military base to debrief before starting to catch their flights home.
Britain is among other countries to have also announced partial troop withdrawals after nearly a decade of war, but the Canadians were the first major troop contributor to start sending forces home this year.
On Tuesday, Canada handed control of their last district to US forces in a flag-lowering ceremony, a key symbolic step in the drawdown process, although the Americans had been in place for weeks.
Last month, US President Barack Obama announced that he would withdraw 33,000 troops from Afghanistan by the end of 2012, while France and Belgium have joined Britain in stating that they will soon bring some soldiers home.
All foreign combat forces are due to leave by the end of 2014 and hand security to Afghan forces.
Canadian commanders insist they have made strong gains since they moved into Kandahar, the Taliban’s birthplace and one of the war’s fiercest hotspots.
Public opposition to the war in Canada has grown, with a poll earlier this year by Vision Critical/Angus Reid indicating that 63 percent of Canadians opposed it, compared to 47 percent in 2010.
Canadian Prime Minister Stephen Harper first pledged in 2008 that troops would leave this year.
After US forces killed Osama bin Laden in Pakistan in May, he said he believed Afghanistan was “no longer a source of global terrorism.”
A separate Canadian training mission involving 950 troops will work in Kabul with Afghan security forces.
Canada will also continue to give aid to Afghanistan, with its overall involvement between now and the end of 2014 expected to cost around US$700 million a year.