The tiny British overseas territory beat an Armenia team including Arsenal's Henrikh Mkhitaryan thanks to Joseph Chipolina's 50th-minute penalty.
It was the first time they had won a match other than a friendly since joining UEFA in 2013 and their players danced with joy at the final whistle.
Yet the night had begun badly for the visitors when the national anthem of Liechtenstein was played before kickoff, prompting a disgruntled tweet from Gibraltar's FA.
"The Gibraltar FA is very disappointed to note that, prior to tonight’s UEFA Nations League match versus Armenia, the national anthem of Liechtenstein was played," it said.
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"The Armenian FA has apologised to the Head of Delegation representing the Gibraltar FA in Yerevan for this oversight and an announcement has been made at the national stadium apologising for the error."
The blunder appeared to motivate the Gibraltar players as they held out against the hosts -- whose best achievement was just missing out on qualification for Euro 2012 -- for the last 40 minutes having had only 28 percent possession and mustering two attempts on target.
Armenia, captained by Mkhitaryan, had 35 shots -- 10 of them on target.
Gibraltar's shock win took them level with Armenia on three points in League D Group 4, six behind leaders Macedonia.
Liechtenstein also have three points.
(Reporting by Neville Dalton, editing by Ed Osmond)
