"I would like to congratulate Pauline Marois on her election victory, and the other candidates for taking part in this democratic process," Harper said in a statement released by the Prime Minister's Office.
The statement goes on to suggest that the federal government will continue to work with the province on jobs, economic growth and sound management of the economy.
- Quebec elects Pauline Marois PQ government
"We do not believe that Quebecers wish to revisit the old constitutional battles of the past," he said.
"We believe that economic issues and jobs are also the priorities of the people of Quebec."
The PQ will form a minority government, bringing to an end nine years of Liberal governance and making Pauline Marois, 63, the province's first-ever female premier. Marois also handily won her riding of Charlevoix-Cote-de-Beaupre.
Interim Liberal leader Bob Rae said on Twitter that Quebec voters "reject separatist project. This is the key point that must not be lost."
The NDP told CBC's Evan Solomon that federal party leader Tom Mulcair spoke to Marois, Charest and Legault to congratulate them on a good and lively campaign.
The federal Liberal party and NDP are not expected to comment officially on the results until Wednesday.
Marois has said a PQ government would work toward sovereignty — taking back powers from Ottawa in areas such as immigration. She's made Quebec's linguistic and cultural identity a key issue in the campaign, to the delight of sovereigntist hardliners.
"In the days that follow, in the weeks that follow, it will be a short delay, I will contact Mr. Harper," Marois told reporters last week while campaigning in Gatineau.
The party has said it wants Quebec to have control over many responsibilities that are usually in the federal domain, from copyright law to international aid funding. If Ottawa refuses, it says, that would bolster the case that Quebec and the rest of Canada must go their separate ways.