The game was billed as a home fixture for the European champions but was played at the Allianz Stadium in Turin owing to COVID-19 guidelines.
The 'hosts' started the game on the front foot and forced Shakrudin Magomedaliyev into two quickfire saves in the 10th minute.
The Azerbaijan goalkeeper soon went down for treatment but was deemed fit enough to keep playing as he continued to pull off fine saves to deny Portugal.
However, Magomedaliyev gifted away the opener with a horrendous error. A routine punch from a cross went awry. His weak punch deflected off his captain Medvedev and into the back of the net.
This was no less than Portugal deserved for their dominant start to the game, but Azerbaijan would have been kicking themselves for the comical way the goal came about.
The second half saw Bruno Fernandes come on for Joao Moutinho, while Gianni De Biassi also made two changes of his own for Azerbaijan.
Portugal upped the ante in a bid to find the second goal, but a combination of poor finishing and inspired saves by Magomedaliyev meant that they failed to kill the game off.
Bernardo Silva, Joao Felix and Bruno Fernandes all came close for Portugal but their defense was very rarely threatened. Despite the sustained pressure in the second half, the Iberians failed to add to their advantage.
Nevertheless, the victory takes Portugal joint-top of Group A ahead of their next fixture with fellow group leaders Serbia on Saturday. Up next for Azerbaijan will be a 'friendly' fixture with Qatar, where they will be looking to get back to winning ways.
Here are five talking points from the game.
#5 Even in victory, Portugal failed to truly impress
Fernando Santos is the most successful manager in the history of the Portugal national team. However, the 66-year-old has built his success on a pragmatic method that prioritizes compactness over flamboyance.
Playing against a team ranked 108 in the world and without any marquee player meant that Portugal were expected to dominate from start to finish.
That was exactly what happened, particularly in the first half when it looked like the Selecao were going to run roughshod over the Eastern Europeans. However, their momentum slowed down in the second half, and there were several periods of indecisiveness from the Portugal players.
The gruelling nature of this season might have played a part. However, even the introduction of fresher players late in the game did not do much to improve the cohesiveness of their play.
Despite the unconvincing display, victory is all that matters for the European champions. Having said that, they have to significantly up their game, otherwise they run the risk of being found out by a better side.
#4 Azerbaijan's goal drought continues
Azerbaijan are not exactly famed for being a footballing powerhouse, and it came as no surprise that they did not really threaten the Portugal goal.
They had just 32% of the ball against their more illustrious opponents and failed to register a single shot on target.
This blank means that Azerbaijan have now gone six games without a goal, with their last goal coming back in September 2020 when Maksim Medvedev's 29th minute strike gave them a 1-0 away victory over Cyprus.
Since then, they have gone over 10 hours without finding the back of the net and did not come close to doing so against Portugal.