Niall Henderson's 11th-minute goal put Newry on the victory trail at Drumahoe.
Henderson shot in after Kevin Keegan's free-kick was only half cleared but Paul Brown quickly replied with a close-range goal for Institute.
On 33 minutes Paul Keenan slammed in Newry's second goal after Richard Clarke's cross had been headed back by Chris Morgan.
Newry made sure of the win when visiting skipper Clarke set up Keegan to make it 3-1.
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