Nicolae Timofti, 63, a relatively politically neutral figure, was put forward by the ruling Alliance for European Integration to break the impasse caused by communist opposition to its previous candidate, an Alliance leader.
He won over three communist defectors to bolster the three-party ruling coalition's 59 votes, giving him 62 votes in the 101-seat chamber.
The EU's foreign policy chief Catherine Ashton, in a joint statement with Stefan Fule, the EU's enlargement commissioner, said the vote would open up dialogue in the country.
Wedged between Ukraine and European Union member Romania, with which it shares a common language, Moldova is one of Europe's poorest states with an average salary of US$270 per month.
It looks to wine and vegetable exports and inflows of cash from thousands of Moldovans working abroad to sustain an economy that is heavily reliant on Russian energy imports.
But despite its poverty, Moldova, which has a population of 4 million, is pressing for association status with the EU and has received plaudits from Brussels for its economic reform plans.
In a swift reaction to the election, Romanian President Traian Basescu said he had assured Timofti of Romania's support for reform in Moldova and for moving closer to the EU.
A new leadership could also help resolve the status of Transdniestria, a strip of land on Moldova's eastern border controlled by pro-Moscow separatists for the past 20 years.
Transdniestria, which has no international recognition as an independent territory, itself elected a new leader last December, increasing prospects of a long-term settlement.
In his speech before the vote, Timofti pledged to maintain strategic ties with the United States, Russia and Germany, as well as strive for a settlement of the Transdniestria problem.
He pledged to combat large-scale systemic corruption which is rife in Moldova as in several of the former Soviet republics.