Her rival, incumbent President Ivo Josipovic of the Social Democratic Party, came in second with 49,57 percent, the commission said.
Voter turnout stood at 58,91 percent of the voters registered in the country and abroad.
Kolinda Grabar-Kitarovic, 46, previously served as a NATO assistant secretary general, minister of foreign affairs and was ambassador to the United States.
Croatia held its sixth presidential election since 1990, when the first democratic elections were held in the country after it became independent from Yugoslavia.
The first round of the vote on Dec. 28, in which 4 candidates had competed, resulted in a run-off between incumbent President Ivo Josipovic and Kolinda Grabar-Kitarovic, when Josipovic enjoyed a narrow lead with 38.46 percent votes, followed by Grabar-Kitarovic, who got 37.22 percent votes.
The president is elected for a five-year term in Croatia. According to the country’s constitution, a candidate can serve as president for a maximum of two terms.
Josipovic has been president since 2010; his term expires on Feb.18. Inaugural ceremony, at which the new president will take office, will be held same day.
In Croatia, the president cannot veto laws but has a say in foreign policy and defence.
After six years of recession, unemployment is running at 19 percent in the ex-Yugoslav republic of 4.4 million people, which joined the European Union last July. High taxes and poor administration hamper business and the economy is not expected to grow in 2015.
"I expect a certain shift in foreign policy, with a little more focus on NATO and the EU and a little less on the (Balkan) region," said Andjelko Milardovic of the Institute for Migrations, a Zagreb-based think-tank, adding the result was a pointer to the parliamentary election.
Grabar-Kitarovic campaigned on the need for a change of course and a more active head of state to help the country overcome its worst economic crisis since independence in 1991.
The HDZ ruled Croatia from its first democratic election in 1990 until its founder, President Franjo Tudjman, died in December 1999. Since then it has alternated in power with the Social Democrats but has never regained the presidential post.