"Kuwait is an influential partner in the region and we are very pleased that this agreement has been reached for the benefit our respective countries," MacKay said in a statement.
He was speaking after he signed a deal during a two-day visit to Kuwait for logistical support from the Gulf nation.
Canada officially ended its nine-year combat mission in Afghanistan on Thursday, closing the curtain after the deaths of 157 troops.
The departure of nearly 3,000 soldiers, who took on some of the heaviest fighting in the southern province of Kandahar, comes as Western forces begin to announce gradual drawdowns of troops ahead of a full withdrawal in 2014.
After spending more than $11 billion on the war and with popular support waning at home, most of the Canadian soldiers, based mainly in the dangerous battleground of Kandahar, have packed up and gone home.
"The movement of equipment and vehicles from Afghanistan requires access to both an airport and sea terminal for the transhipment of materiel back to Canada," the Canadian defense ministry said in a statement.
"The establishment of this support presence in Kuwait allows this to happen in a safe and controlled environment."
Until last year, Canada was using a base situated in Dubai to support its operations in Afghanistan. But it was forced to leave the base amid differences with the United Arab Emirates over increasing commercial flights between the two nations.
MacKay recalled that Canada had deployed some 4,000 troops during the first Gulf War in 1991, and "our friendship has grown stronger over the past twenty years," he added.
A separate Canadian training mission involving 950 troops will continue to 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 $700 million a year.