Slovakia top Group C with 18 points from six games ahead of European champions Spain, who have 15 after beating Belarus 1-0 away, and Ukraine on 12 after a 3-0 home win over Luxembourg.
The Slovaks opened the scoring in the eighth minute when Salata, named as a last-minute starter after Jan Durica was ruled out due to injury, beat the offside trap to head home.
Hamsik doubled the lead in the 38th when he latched onto Robert Mak's through ball, rounded the keeper and slotted home.
Macedonia pulled a goal back in the 69th minute when the unmarked Arijan Ademi tapped the ball into the net after a corner was nodded on from the near post.
The visitors were unable to capitalise on the goal and were reduced to 10 men with six minutes left when Feran Hasani was sent off for a second yellow card.
"They weren't pushing so hard, we were just playing our game," Slovakia midfielder Viktor Pecovsky said. "In the second half we stopped playing a little bit but we managed."
(Reporting by Michael Kahn,; Editing by Ken Ferris)
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