All the action was confined to the first-half as United got the lead through Ranty Martins' goal from a spot-kick in the 20th minute, while Shylo Malswamtulunga settled the issue seven minutes later.
Ranty stayed as the top-scorer in the league with 25 goals.
United SC with 41 points from 25 matches pipped Pune FC to be behind league leaders Churchill Brothers and East Bengal, while the Shillong outfit remained at 10th with 25 points from as many matches.
Ranty converted the spotkick without much fuss to give them a 1-0 lead. Seven minutes later, Ranty set it up for Vincent who made a run behind the defence and made a square pass to Malswamtulunga who slotted it into an empty net.
Both the teams had some fine chances in the second-half but the goalkeepers, Subrata Paul of United SC and Ralte of Lajong, stood out under the bar.