It was sweet revenge for Boro boss Tony Pulis who was sacked by the Baggies last November.
The home side were frustrated right until the end as they missed a host of chances to put Darren Moore's side to the sword at the Riverside.
Martin Braithwaite and Ryan Shotton were the biggest culprits as the Wearsiders were by far the dominant side and should have taken all three points.
Braithwaite missed the best chance of the first half as the home side were in total control of the game.
Aden Flint towered above everyone in the box to head down for the forward who blazed over from six yards out for a deserved lead going into the break.
Boro flew out the blocks after the break when Brit Assombalonga's cross was headed over from close range by Ryan Shotton.
Dwight Gayle should have put the Baggies ahead moments later.
The on-loan striker was put clear by Matty Phillips, but he hesitated and scuffed his shot high over the bar.
But deep into stoppage time, Ayala was the quickest to react to Mo Besic's free-kick that fell kindly for him in the box.
The Spaniard fired home past Sam Johnstone to send Boro three points clear of Leeds, who can reclaim top spot with a win at Norwich.
The defeat is bitter blow for Moore who was desperate to go on a long unbeaten run after a convincing 7-1 hammering of QPR last Saturday.
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