Mr Pellegrini, 48, defeated the pro-Western Ivan Korcok, a former diplomat, with 53% of the vote.
A former prime minister, he is an ally of nationalist Prime Minister Robert Fico, and shares the PM’s dovish attitude towards Russia.
Mr Fico and his allies now control Slovakia’s parliament, government and soon the president’s office.
Slovakia had been one of Ukraine’s staunchest allies before Mr Fico came to power in October on a pledge to halt supplies of Slovak Army military stocks to Kyiv. With Mr Pellegrini replacing Mrs Caputova, Ukraine has now definitively lost a voice of support in an EU and Nato capital.
Mr Fico has called for an end to Western military support for Ukraine, an immediate ceasefire and peace talks with Moscow. Mr Fico said recently President Vladimir Putin had been “unfairly demonised” and argued admitting Ukraine to Nato would mark the beginning of a third world war.
Mr Pellegrini’s campaign echoed some of that Moscow-friendly rhetoric, accusing Mr Korcok of being a warmonger who would send Slovak soldiers to fight in Ukraine – a constitutional power the president does not have.
Once Mrs Caputova steps down in June, there will be no longer be any high-level official in Slovakia – a country which barely a year ago donated its entire fleet of MiG-29 aircraft to Ukraine – who unequivocally backs Kyiv’s effort to defend its territory with force.
The liberal pro-Western opposition also accuses Mr Pellegrini – as head of the coalition Hlas party and chairman of parliament – of remaining silent as Mr Fico took a wrecking ball to Slovakia’s criminal justice system, notably abolishing the Special Prosecutor’s Office, which was set up 20 years ago to investigate serious corruption and economic crime.
It had tried a number of senior officials in Mr Fico’s Smer party, and had been overseeing the prosecution of those believed to be responsible for the murder of investigative journalist Jan Kuciak and his fiancée Martina Kusnirova in 2018.
The killings were a seismic event in Slovak politics. The fallout ended Mr Fico’s second premiership in 2018 and led to the liberal, pro-Western Zuzana Caputova being elected president on a wave of popular anger at official corruption and organised crime.
Robert Fico’s government recently set its sights on Slovakia’s public broadcaster, submitting plans to abolish the institution and replace it with one under virtual state control. Those plans were put on the back burner after a surprisingly poor showing from Peter Pellegrini in the first round of the presidential election two weeks ago.
The opposition fears a reinvigorated Robert Fico will resubmit them – and they say President-elect Pellegrini is unlikely to stand in his way.