But it mattered little to the Gibraltar supporters and players, who lingered on the pitch to savor the draw after the final whistle.
"This is a proud result for Gibraltar and the players gave me so much more than 100 percent," Gibraltar coach Allen Bula told UEFA. "It was a dream to play our first international friendly and now we have another dream come true thanks to this great result."
Despite missing several of its first-choice players, Slovakia started the match as the clear favorite. It was ranked 65th in the world and 27th in Europe and coming off a 2-0 win last week in Poland.
But Gibraltar did well to resist with a scrappy defense that conceded the ball to Slovakia, but also blunted its attack.
"Just few days ago, we were enjoying a victory at Poland after a very good performance," Slovakia coach Jan Kozak said. "But that's another face of football. The result is a huge disappointment for me. We missed quality and that was reflected in our play."
Slovakia was without key players including Napoli midfielder Marek Hamsik and Liverpool defender Martin Skrtel. Goalkeeper Tomas Kosicky, defenders Martin Juhar, Pavol Farkas, Lukas Stetina and Branislav Ninaj and striker Adam Zrelak made their international debut.
Gibraltar goalkeeper Jordan Perez saved Freiburg midfielder Karim Guede's 12th-minute strike in the Slovakia's clearest chance until stoppage time when Kornel Salata headed a corner kick off the crossbar.
The best shot Gibraltar could muster was an excursion down the right flank finished by Adam Priestley sending in a cross that was deflected into the hands of Kosicky in the 10th.
Gibraltar plans to host the Faroe Islands and Estonia in March in its Victoria Stadium.
Spain has long-standing claims on Gibraltar, which was captured by Anglo-Dutch naval forces in 1704 and ceded to Britain in the 1713 Treaty of Utrecht.
The Gibraltar Football Association, which was founded in 1895, applied to FIFA for membership in 1997 with the backing of England, but the world governing body delegated the decision to UEFA.
The match came after months of rising tensions between Spain and the tiny colony perched on a rocky outcropping near the western edge of the Mediterranean Sea.
Earlier on Tuesday, Britain's Foreign Office said it was summoning Spain's ambassador over what it calls ongoing incursion in Gibraltar's waters by a Spanish research vessel. This was after Spain retaliated to an artificial reef built by Gibraltar it said hurt its fishermen by beefing up security at the border.