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Lithuania pummelled the San Marino goal throughout the first half as Novikovas, Cernych and Lukas Spalvis weighed in with chance after chance, but they couldn't add to their tally by the break.
In a shock turn of events, the visitors - who had not scored an away goal since 2001 - equalised five minutes before the hour through Matteo Vitaioli's free kick, a goal which prompted wild celebrations among the Sammarinese contingent.
Lithuania grew increasingly desperate in a bid to find a winner against one of the world's lowest-ranked sides, and were given a boost when Nicola Chiaruzzi was dismissed for a second yellow card with two minutes left.
The hosts' blushes were then spared right at the death when Novikovas's cross fell to Spalvis, who drilled home from close range to break San Marino's hearts.