With back-to-back wins, the Dynamos kept themselves in contention for a last four berth with 13 points from 11 games, which places them at fifth position in the eight-team table.
While Mumbai City FC are only a point behind from same number of matches, their fifth defeat pushed them to the bottom of the table.
Mulder found the target in the 44th minute while striker Junker struck in the 50th minute to seal the issue in Dynamos' favour at the floodlit Jawaharlal Nehru Stadium.
Manish, who came in as a substitute, made it worse for the visitors as he scored in the 90th minute.
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For the visitors, former India international Abhishek Yadav, who came in as a substitute, pulled one back for the in the 86th minute.
Mulder, who had also scored in the side's last game, struck for the hosts with a rasping right-footed volley after receiving the ball from Francis Fernandes just a minute before the breather.
Dos Santos then go into the thick of things as he headed one in to the right side of the post after meeting a fernandes cross inside the 18-yard box.
Following the triple-strike from the Dynamos, the match was as good as over, with the Mumbai defence wilting at the face of the relentless pressure put on by the hosts.