The result saw Kenya go joint top with Ethiopia who had earlier beaten South Sudan 2-0. With the two teams having identical results after the group games, the winner of the group will be decided by the toss of a coin.
Stars made one change with Musa Mohammed coming on in place of the suspended Aboud Omar while Allan Wanga was handed the captaincy in a bid to boost his confidence after a poor game against South Sudan last week.
The final group games had been moved to Nakuru and the resident of the Rift valley capital responded with a huge turnout that rallied the home side.
Stars got off to the perfect start when Francis Kahata was hauled down in the box with the referee pointing to the spot in the fifth minute.
Defender Jockins Atudo who had scored one penalty and missed another in the previous game made no mistake rifling the ball past Zanzibar keeper Rashid Abdalla.
Man on The Match Jacob Keli then created a chance out of nothing on the quarter hour mark turning his marker inside out but Abdalla saved his effort with his feet.
Having been under the cosh for most of the first half hour, Zanzibar grew back into the game with Masoud fashioning their best chance of the first period for Suleiman Kassim but his shot hit the side netting on 32 minutes.
Keli had a chance to put the game to bed on 52 minutes but he lashed his shot wide with the goal at his mercy.
Wanga made it 2-0 with a beautifully worked goal on the hour mark collecting an impudent Keli back-heel and firing the ball past Abdalla. It was welcome goal for Wanga who has struggled all tourney and his celebrations told how much it meant to him.
Stars needed another goal to secure top spot but in the end; they needed Duncan Ochieng to make a fine stop to preserve their clean sheet.
Kenya will now rely on the lottery of a toss coin while Zanzibar face a nervous few days as they wait to find out whether they qualify as one of the best third placed teams.