The moves were announced Sunday before the finale of a three-game series with the NL West-leading Dodgers.
Thornton missed 16 games because of an oblique strain on his right side. The Red Sox acquired him from the White Sox on July 12. He is 0-4 with a 3.47 ERA in a combined 50 relief appearances with Boston and Chicago. Thornton is one of four lefties in the Red Sox bullpen, along with Craig Breslow, Franklin Morales and rookie Drake Britton.
In Villarreal's only appearance following his callup last Monday, he walked San Francisco's Marco Scutaro with the bases loaded to force in the winning run in a 3-2 loss on Tuesday.