Bale struck his 32nd goal for Wales six minutes from time, rising to head home after Joe Allen's shot had been deflected high into the Cardiff air.
Azerbaijan are ranked 109th in the world – a whopping 85 places below Wales – and their only competitive away wins came in the Faroe Islands and San Marino.
But Wales, who could not afford to drop points after June defeats in Croatia and Hungary, were poor throughout and there was more relief than satisfaction at the final whistle.
Manager Ryan Giggs had labelled it as a must-win game and fielded an entirely different back four to the one beaten in Budapest.
Azerbaijan would certainly have been wary of Wales' forward power, especially as they had conceded five goals at home to Slovakia in their previous qualifier.
Bale was also buoyed by being back among the goals at Real Madrid, while James' confidence was high after making a tremendous start to his Manchester United career.
James was into the action as early as the second minute when his curtailed run ended with a Wilson free-kick and Rodon almost making a dream start at the far post.
Bale allowed Lawrence to volley wide, but Wales were soon running down cul-de-sacs and their rising frustration was illustrated when Wilson left his mark on Richard Almeida.
Referee Trustin Farrugia Cann gave Wilson the benefit of the doubt and did not even show a yellow card, although another referee might have viewed it as a stamp and worthy of punishment.
Bale dropped deeper as Wales sought a route to goal, but there was little cause for optimism until Pashayev's bizarre intervention.
The Wales captain turned infield to strike a shot which hit Dmitri Nazarov and spun into the air.
Azerbaijan appeared to have little to worry about, but Salahat Agayev came rushing out of his goal and the ball struck Pasahayev's head and trickled in to an unguarded net.
That eased some of the home nerves, but Wales did not manage an on-target attempt until first-half stoppage time.
Lawrence accepted Allen's pass and cut on to his left foot, but Agayev saved comfortably.
Azerbaijan had their own moment of good fortune when Emreli escaped with a swinging arm on Mepham, the Maltese referee again showing his lenient side.
Wales were still struggling to get out of first gear when Azerbaijan landed a sucker punch.
Taylor's mistake allowed Ramil Sheydaev to release Emreli, who had the freedom of the Wales half to run into.
Emreli's effort was tame, but Wayne Hennessey failed to hold the shot and the rebound was summarily dispatched.
Wales poured forward in search of a winner, but time was running out until Bale – as he has so often done in the past – proved their saviour.