Borisov's European Development of Bulgaria (GERB) party won around 32 percent, the exit polls showed, ahead of the Socialist Party (BSP), seen as closer to Russia, on around 28 percent.
Whether the burly former firefighter and mayor of Sofia, 57, can form a stable coalition remains to be seen, however.
The European Union's poorest country, where the average monthly salary is just 500 euros ($540) and corruption is rife, has been beset by instability for years.
Borisov, 57, once a bodyguard for Bulgaria's last communist leader, has long dominated national politics, serving as premier from 2009 to 2013 and again from 2014 to 2017.
In between, the BSP was in power for barely a year.
Both times Borisov quit early, first in 2013 after mass protests and then last November after his candidate for the presidency was beaten by an air force general backed by the BSP.
Forming a coalition this time will be tough.
The nationalist United Patriots looked to have come third with around eight percent, although the Movement for Rights and Freedoms (MDL) party, representing Bulgaria's Turkish minority, may have beaten them.
But its weak showing will be a relief to observers who thought that a Socialist victory might see NATO member Bulgaria tilt more towards Russia.
Moscow, which has long had close cultural and economic ties with Bulgaria, has been accused of seeking to expand its influence in other Balkan countries in recent months.
Ninova had said she was not content with Bulgaria being a "second-class member" of the EU and that she would veto an extension of sanctions imposed by Brussels on Moscow.
"We are the party that ushered Bulgaria into the European Union and NATO and we stand by (our obligations in) these organisations," she told AFP in a recent interview.
The campaign also saw a spat erupt between Bulgaria and its neighbour Turkey.
Bulgaria is home to a 700,000-strong Muslim minority, most of them ethnic Turks, while at least 200,000 ethnic Turks with Bulgarian passports live in Turkey.
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