Portugal, first round casualties at the World Cup, were sorely missing their skipper Cristiano Ronaldo but despite the Real Madrid star's absence the 1-0 loss to a team ranked 71st in the world was a major embarrassment for Paulo Bento's side.
Albania, who have failed to qualify for a European Championships in half a century, humbled the mighty Portuguese in their own back yard.
Slavia Prague forward Bekim Balaj struck the killer blow shortly after the restart, with the home side walking off the pitch in Aveiro at the final whistle to boos from their supporters.
"We've started qualifyng badly, now we have to pick ourselves up. We have to improve."
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Down on Portugal's Algarve coast, minnows Gibraltar were given a lesson on their introduction to competitive internationals as a UEFA member by Poland as Bayern Munich's Robert Lewandowski scored four times in a 7-0 romp.
In Dortmund, Germany, beaten last week in a friendly by Argentina, got their qualifying campaign up and running with a 2-1 defeat of a spirited Scotland.
A goal in each half from Bayern Munich attacker Thomas Mueller ensured they won their first competitive fixture since the World Cup.
But the visitors failed to clear a corner four minutes later and Mueller capitalised to thump home his 24th international goal.