Sevilla went top of LaLiga earlier in the day with a 2-2 draw against Alaves, a stoppage-time equaliser sending it to the summit.
But Sevilla and Real Sociedad are now just two points above Atletico, which claimed victory from one of only two efforts on target at Wanda Metropolitano.
Felipe rose to meet Yannick Carrasco's near-post corner and turn it home, providing a dramatic finish to what had otherwise been a dour encounter on Sunday (AEDT).
