Lithuania’s triumph comes off the back of a 2:0 over the San Marino last month as the Baltic nation now eyes off Slovenia this Sunday.
After a quiet first half Saulius Mikoliūnas was brought onto the field at the 63rd minute, only then to kick the game’s only goal a quarter of an hour later.
It was the 30-year-old’s 5th International goal and came almost a year to the day he kicked his most previous on the same ground.
Deivydas Matulevičius meanwhile was credited with the goal assist while Egidijus Vaitkūnas and Vytautas Andriuškevičius both received yellow cards in the eventful half.
Estonian star Ken Kallaste was the only player to receive a red card, a reflection of the rivalry displayed between the Baltic nations in the mutual obsessed sport.
Overall Lithuania was credited with 53% of the possession while Estonia was granted a lead in the corner kicks tally 6:4.
In other games, England leapfrogged Lithuania with a handy 5:0 triumph over San Marino before 55,000 at the Wembley Stadium in London.
Interestingly Switzerland, fresh from a FIFA World Cup appearance, was handed its second straight defeat thanks to the accuracy of Slovenian veteran Milivoje Novaković (final scores 1:0).
Lithuania: Saulius Mikoliūnas (76’).
Estonia: Ken Kallaste (86’).
Lithuania: Vytautas Andriuškevičius (61’), Egidijus Vaitkūnas (87’).
Estonia: Sergei Zenjov (33’), Ken Kallaste (64’).
Lithuania: Saulius Mikoliūnas on for Mindaugas Kalonas (63’), Ričardas Beniušis on for Deivydas Matulevičius (90’).
Estonia: Sergei Zenjov on for Henrik Ojamaa (64’), Konstantin Vassiljev on for Joel Lindpere (76’), Ats Purje on for Martin Vunk (80’).
Location: LFF Stadium, Vilnius.
Referee: Clos Gómez (Spain).
2014 Lithuanian National Men’s Fixture:
Lithuania v Slovenia (12 October, 2014).
Switzerland v Lithuania (15 November, 2014).
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