Chances were scarce for much of the match at St James's Park but the France international midfielder settled the game with just two minutes to goal by finding the bottom corner
After a first half in which chances were few and far between, the Magpies stepped up the pace after the break but left it late to go in front at St James's Park, with substitutes Ayoze Perez and Gabriel Obertan combining well before Sissoko stroked the ball into the bottom right-hand corner from distance.
There was an early scare for the home side when Yoan Gouffran was brought down by Sergio Canales just outside the area. The winger appeared to be holding his knee as he hit the deck but limped back into the game after receiving lengthy treatment.
Chances were at a premium for much of the first period and Imanol Agirretxe failed to make his opportunity count just before the half-hour mark when he could have lofted the ball over goalkeeper Tim Krul.
Emmanuel Riviere had Newcastle's best chance of the first half, firing over before Agirretxe almost capitalised on a missed headed clearance by Fabricio Coloccini.
Gouffran was withdrawn at the break to be replaced by Rolando Aarons and the hosts began to look more dangerous in attack. The youngster's first major contribution was to beat three Sociedad players on a charge forward, only to see his eventual effort deflected behind.
Mike Williamson worked goalkeeper Geronimo Rulli with a goalbound header from a corner on the hour but it was Sissoko who settled matters, finding the net two minutes from time to send Newcastle into their Premier League opener against champions Manchester City with a timely confidence boost.