Goals from Saul Niguez, Diego Costa, Alvaro Morata and Thomas Partey were enough to send Atletico back to within 10 points of LaLiga leader Barcelona and five ahead of third-place Real Madrid, which plays on Monday (AEDT).
It was a commendable display from the visitors, who lost back-to-back matches to Juventus and Athletic Bilbao before the international break to effectively end any hopes of finishing the season with a trophy to add to last August's UEFA Super Cup triumph.
Saul, having been denied by a good Fernando Pacheco save, had better luck with only five minutes played when he drilled a left-footed shot beneath the goalkeeper after being sent clear by Antoine Griezmann.
Atleti doubled its lead only six minutes later, Costa collecting Koke's pass 25 yards out before bending a fine strike beyond the static Pacheco and in off the right-hand post for his first league goal since November.
The visitors eased off and nearly paid the price before the break, with Saul heading the ball off the line after Tomas Pina flicked on a corner, and Alaves was furious when Thomas Lemar escaped a second yellow card for a high foot as its pressure continued in the second half.
Those frustrations were compounded moments later when Lemar slid a fine throughball into the path of Morata, who side-footed past Pacheco with aplomb from 12 yards.
Pacheco denied Griezmann a fourth with a fine one-handed stop that sent his attempted chip onto the left-hand post, but Diego Simeone's side reserved its best moment until last, with Thomas bending a stunning strike in off the woodwork with six minutes left.