Standing beside President Juan Manuel Santos, Harper said negotiations that began in 2008 had been ratified by both governments.
A release said the agreement will "help Canadian businesses improve access to an emerging market of 45.5 million people and an economy with a high growth potential."
Bilateral trade between the two countries totaled $1.4 billion last year, up 32 percent since 2005, the release said.
Harper also said Canada would maintain its support of U.N. efforts to improve human rights and aid to Colombia through UNICEF and the U.N. High Commissioner for Refugees.
Harper is on a six-day tour through South and Central America. He spent two days in Brazil and was due to depart for Costa Rica Wednesday night and Honduras on Friday.