Saul Niguez scored the only goal in the first half to make up for their group-stage exit from the Champions League and extend the Rojiblancos' unbeaten run in LaLiga to a history-making 19th match.
Antoine Griezmann suffered a hamstring strain the midweek draw with Chelsea and was forced to sit out the trip to the Benito Villamarin, while Fernando Torres was relegated to the bench.
The pair's presence would likely have made little difference to a one-sided start to proceedings as mid-table Betis, now winless in six LaLiga matches, dominated the early possession and territory.
But midfielder Saul poked home with his side's first chance to calm the nerves and put the visitors on course for a third consecutive league victory.
Diego Simeone's men were content to repel Betis' occasional incursions after the restart in climbing back into third, two points ahead of rivals Real Madrid.
Simeone's four changes included recalls for Diego Godin and Sime Vrsaljko to a defence that was spared by a tame Ryad Boudebouz finish in the third minute.
Betis kept the pressure on over the opening 25 minutes and saw Joaquin's free-kick flash dangerously across the face of Jan Oblak's goal.
Having survived that examination, the visitors needed only one chance to take the lead against the run of play just before the half-hour mark.
Vrsaljko received Godin's raking pass out to the right and whipped an enticing ball across the face that somehow evaded an initial clutch of players. An untracked Saul was the beneficiary, stretching to tap in at the far post.
And they might have doubled the advantage almost instantly, but Angel Correa passed up better options in shooting straight at Antonio Adan.
Unbroken by Atletico's first half sucker-punch, Betis threatened again after the break as Sergio Leon fired off target from a narrow angle.
Cristian Tello went closer with a stinging drive soon after, only for Oblak to spectacularly claw it away from the top-right corner.
That superb save proved to be the Slovenia goalkeeper's last real test of a largely untroubled second half, the away side shutting the gate as they have done numerous times throughout their impressive unbeaten run in the league.