Play was held up for several minutes after visiting Bosnia fans hurled several flares on to the pitch in the 14th minute. The officials had to wait for the billowing smoke to clear before allowing the contest to continue.
The result left Bosnia third in the group on 17 points, two behind second-placed Greece who secured a playoff berth with a 4-0 home win over Gibraltar.
Group winners Belgium, who had already sealed automatic qualification for next year's tournament in Russia, beat Cyprus 4-0 to finish on 28 points.
The Estonians finished fourth with 11 points.
Bosnian forward Izet Hajrovic broke the deadlock shortly after half-time when he smashed a volley past goalkeeper Mikhel Aksalu, who produced three fine saves while the home side were on the back foot.
Midfielder Ilja Antonov equalised with a rasping low shot from 20 metres in the 75th minute after picking up a loose ball and rifling it past Bosnia's Asmir Begovic.
But Hajrovic was on target again almost ten minutes later, drilling an arrowed shot past Aksalu after being put through by Roma striker Edin Dzeko, who came off the bench for a makeshift Bosnian side missing the bulk of their regular starters.
(Writing by Zoran Milosavljevic in Belgrade; Editing by Christian Radnedge)
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