Neither goal was seriously threatened until the 88th minute when Zayatte put the ball into his own net from a blistering Ashley Young cross.
Then in injury time there was controversy at the other end as referee Steve Bennett seemingly awarded a penalty and then changed his mind.
From the off there was drama as, after going up for a challenge with Brad Friedel, Nick Barmby forced Nigel Reo-Coker to put the ball in the back of his own net with just five minutes on the clock.
However, the goal was ruled out by referee Bennett after Barmby was adjudged to of fouled the American keeper.
Benard Mendy created a chance after quarter of an hour as the Frenchman skipped down the right and fired in a cross towards Peter Halmosi only for the Tigers' record signing to fail to connect with the ball.
Curtis Davies nearly scored a spectacular own goal towards the end of the half as Ian Ashbee swung in a cross from the right but the Villa defender managed to thump his header just wide of post.
After already being booked, Zayatte was given a stern warning by referee Bennett after barging Gabriel Agbonlahor off the ball minutes before the break.
As the first half came to a close neither team could find a breakthrough with the visitors playing the neater football against a battling Hull side.
Stiliyan Petrov was booked on the hour-mark after protesting that his blistering shot from 25 yards received a deflection off a Hull defender on its way past Boaz Myhill's left-hand post.
After Hull had taken control of the game, Villa broke away and snatched the points with two minutes left on the clock as Ashley Young raced down the right and played in a low cross to Agbonlahor.
Zayatte managed to get in front of the England international but he could only turn the ball into the back of his own net from four yards.
Then in injury time, Hull seemed to have been awarded a penalty as Bennett pointed to the spot for a handball on the line by Ashley Young, but after deliberating with his assistant the official correctly decided that it hit the crossbar.