La Liga’s second-placed club could have closed the gap to three points after Barcelona drew 2-2 with Valencia, but they struggled to break down Betis.
The match was settled by Sergio Canales’ 65th-minute penalty after defender Filipe Luis had handled.
Morata, signed from Chelsea on loan this month, had four efforts on goal.
France World Cup winner Antoine Griezmann went close for the visitors with a second-half strike that came off the post.
This was Atletico’s first loss in the league in 19 games and they remain six points behind Barcelona. Third-placed Real Madrid could close the gap to Diego Simeone’s side to two points if they defeat Alaves late last night.