Sixty-year-old challenger Efrain Alegre of the Concertacion center-left coalition garnered nearly 27.5 percent despite having gone into the vote with a narrow lead in opinion polls.
The outcome bucked a recent anti-incumbency trend in Latin American elections with voters repeatedly punishing establishment parties, often in favor of leftist rivals.
The Colorado Party has governed almost continually since 1947 -- through a long and brutal dictatorship and since the return of democracy in 1989, but has been tainted by corruption claims.
Pena's political mentor, ex-president and Colorado Party leader Horacio Cartes, was recently sanctioned by the United States over graft.
Pena thanked Cartes in his first public address as president-elect for his "stubborn dedication to the party," to loud cheers from supporters at party headquarters.
Conceding defeat, Alegre stated: "The effort was not enough."
Around 4.8 million of Paraguay's 7.5 million inhabitants were eligible to vote Sunday for a replacement for President Mario Abdo Benitez, who is leaving office after a constitutionally limited single five-year term.
They also voted for new lawmakers, with the Colorado Party winning the highest share of the upper house Senate votes at 43 percent.
Voting is mandatory in Paraguay, though only 63 percent turned out.
Key issues for voters were endemic corruption, a spiraling crime problem and poverty.
Ties to Taiwan
On the international stage, Pena's win defuses fears that Paraguay would end diplomatic relations with Taiwan in favor of China.
Unlike his challenger, Pena had vowed to continue recognizing the self-ruled democracy, which counts a dwindling number of allies as Beijing pushes to isolate it.
Alegre had mooted a shift to China for the economic and trade benefits.
On Monday, Taiwan's President Tsai Ing-wen congratulated Pena on his win.
"I look forward to furthering our countries' longstanding relationship and to seeing the government and people of Paraguay prosper under your leadership," she said on Twitter.
Pena has also promised to move Paraguay's embassy in Israel from Tel Aviv to Jerusalem.
Paraguay had previously moved its embassy in 2018, under Cartes, but reversed its decision within months, raising the ire of Israel.
"Yes, I would go back to Jerusalem," Pena told AFP before the vote.
"The State of Israel recognizes Jerusalem as its capital. The seat of the Congress is in Jerusalem, the president is in Jerusalem. So who are we to question where they establish their own capital?"
Moving an embassy to Jerusalem is highly contentious. Israel claims all of Jerusalem as its capital while Palestinians view east Jerusalem as the capital of their future state.
Hoping for 'least worse'
Like challenger Alegre, Pena is socially conservative, with strong stances against abortion and same-sex marriage in an overwhelmingly Catholic nation.
Alegre had repeatedly pointed to corruption in the Colorado Party.
Paraguay is ranked 137 out of 180 countries on Transparency International's Corruption Perceptions Index.
Paraguay's GDP is expected to grow 4.8 percent in 2023, according to the central bank, and 4.5 percent, according to the International Monetary Fund -- one of the highest rates in Latin America.
But poverty plagues a quarter of the population.
Paraguay's Indigenous groups and inhabitants of squalid shantytowns feel especially neglected, and many had said they would not vote.
Pena had pledged to create half-a-million jobs, without saying how.
"From tomorrow (Monday) we will begin to design the Paraguay that we all want, without gross inequalities or unjust social asymmetries. We have a lot to do," he said in his victory speech.
Crime is also a concern, with an anti-mafia prosecutor, a crime-fighting mayor and a journalist murdered in 2022 as cartels settle scores.
Experts say landlocked Paraguay -- nestled between Brazil, Bolivia and Argentina -- has become an important launchpad for drugs headed for Europe.
Also in the capital, 60-year-old voter Ana Barros said: "You have to have at least hope, that there will be less crime. It is what I hope as a mother, that the children can study and have work."
© 2023 AFP
