Paulo Bento's side move to within one points of group leaders Russia and all but end Azerbaijan's hopes of qualifying for the World Cup next summer
The visitors dominated from the off, but were forced to wait until the hour mark to take the initiative as Bruno Alves powered a header past Kamran Agayev at the near post before second half substitute Hugo Almeida added a second with 10 minutes remaining.
Danny saw an effort comfortably saved by Agayev and Joao Moutinho fired over the bar from distance as Portugal looked to net early on in an encounter they needed to win.
Moutinho flashed another shot wide from the edge of the 18-yard box and Helder Postiga forced a good save out of Agayev from distance as the visitors pressed Azerbaijan early on.
Postiga directed his header goalbound having met Vieirinha cross, but Agayev was equal to the strikers header as Portugal maintained their intense start midway through the first half.
Azerbaijan captain Rashad Sadygov was forced into a superb last ditch challenge to deny Postiga, while Miguel Veloso saw his curling free kick drift agonisingly wide as the hosts continued to frustrate Paulo Bento's side.
Alves came the closest to breaking the deadlock in the opening 45 minutes, but the powerful centre-back could only see his free kick rebound off the post as Portugal struggled to find a way past Agayev.
The Azerbaijan goalkeeper endured pushing away Postiga's close range diving header as the first half drew to a close with the score at 0-0, and the hosts went into the break.
Azerbaijan's evening was made that much more difficult in the 55th minute when striker Rauf Aliyev was given his marching orders for a second booking as referee Andre Marriner deemed his elbow on Raul Meireles worthy of a red card.
Portugal looked to make their numerical advantage almost instantaneously, but Meireles could only flash his effort from a tight angle wide of the far post before being substituted.
The Seleccao continued to press the hosts and took the initiative in the 63rd minute as Alves headed a Moutinho corner past Agayev at the near post.
Portugal pushed for a second and were rewarded with 10 minutes remaining when Fabio Coentrao pushed forward and expertly picked out Almeida at the back post to head into an empty net to secure all three points.
The 2-0 win for the visitors moves them to within one point of Group F pacesetters Russia, albeit having played two games more, and all but ends Azerbaijan's hopes of qualifying for Brazil 2014.