Niguez jinked past a clutch of Bayern defenders before curling into the corner, giving the home side a narrow first-leg lead to take to Germany.
Bayern dominated the second half, David Alaba hitting the bar from 35 yards and Arturo Vidal’s strike forcing a save.
Fernando Torres poked against the post in a rare counter as Atletico held on.
The teams will meet at Bayern’s Allianz Arena on Tuesday to decide who will meet Manchester City or Real Madrid in the final on 28 May.
Atletico – for so many years in the shadow of illustrious neighbours Real Madrid – have never been crowned European champions, twice losing in the final of the continent’s leading club competition.
Under coach Diego Simeone, Los Rojiblancos have emerged as serious challengers to Spain’s regular duopoly of Barcelona and Real Madrid and have now put themselves in a decent position to create history by winning the Champions League.
With Bayern boasting a remarkable home record of only one defeat in 24 matches, the tie is far from over.
But Niguez – a Spain Under-21 international who has cemented his place in the Atletico side this season – extended the Spanish title-chasing side’s own excellent form at a raucous Vicente Calderon.
The 21-year-old midfielder picked up the ball about 35 yards from goal, dancing through flimsy challenges from Bayern trio Thiago Alcantara, Juan Bernat and Xabi Alonso, then keeping his composure to steer the ball into the bottom corner.