The 33-year-old only made a comeback in the longer format of the game after five years in the first Test against England in Abu Dhabi, smashing a career-best 245.
But since then he has made nought, two, seven, 38 and nought in the remaining five innings of the series, prompting him to call it a day.
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Malik was married to Indian tennis star Sania Mirza in 2010, a wedding widely publicised across Pakistan and India.
"I realised today that this is the right time to leave the place for youngsters and Pakistan have many talented players who can fill in," said Malik, who made his Test debut against Bangladesh in Multan in 2001.
In all, he played 35 Tests, scoring 1,898 runs with three centuries and eight half-centuries.
He has so far taken 29 wickets, with his best figures of 4-33 coming on Tuesday against England in Sharjah, a figure to which he can possibly add a few in England's second innings.
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