Third-placed Albania have 11 points from six games and despite the setback are assured of at least a play-off berth.
Portugal avenged their shock defeat by the Albanians in the reverse fixture at home after Veloso rescued them from a series of misses by Cristiano Ronaldo in Elbasan.
The Real Madrid hitman skewed an inviting cross wide from almost point blank range in the 13th minute, shortly after forcing a good save from keeper Etrit Berisha.
He glanced a header wide on the half hour and it looked like Albania would hang on until Veloso rose above his marker to head home a Ricardo Quaresma corner.
Portugal are at home to Denmark and then away to eliminated Serbia in their last two qualifiers, while Albania are at home to Serbia before they visit out-of-contention Armenia.
(Writing by Zoran Milosavljevic, editing by Pritha Sarkar)
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