Stubb, 46, currently European and trade minister in Finland, will replace Jyrki Katainen, who said in April he would step down to seek a job within the European institutions.
He defeated Social Affairs Minister Paula Risikko by 500 votes to 349 in the second round of polling by members of Finland's national coalition. Industry Minister Jan Vapaavuori, a controversial candidate with a criminal record, came third.
Stubb is a former foreign minister known for his liberal economic stance. Staunchly pro-EU and an advocate of Finland's accession to NATO, he is faced immediately with an economy mired in recession.
Public debt, just under 50 per cent of GDP when Katainen took office in 2011, will this year surpass the European Union limit of 60 per cent, putting Finland's cherished Triple A credit rating in doubt.
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The Finnish economy has been hit hard by a decline in the paper and electronic industries, an ageing population and rising unemployment which reached 8.5 per cent in April.
The crisis in Ukraine and the weak ruble have also affected the Nordic economy which is heavily dependent on trade with neighbouring Russia.
Considered one of the most popular political figures in Finland, Stubb was an advisor to then European Commission president Romano Prodi between 2001 and 2003.
Stubb was also a member of the European Parliament from 2004 to 2008 before being appointed Finland's foreign minister between 2008 and 2011.
Stubb will be thrown straight into campaign mode, with Finland's next general election needing to take place by April next year.
The conservative party -- officially, the Party of National Coalition -- has 44 of parliament's 200 seats. It came first in European elections in May with 22.6 per cent of the vote, ahead of its main rivals, the Centre Party with 19.7 per cent and the eurosceptic and anti-immigration Finns party on 12.9 per cent.