Pena has not played since Saturday, when he felt something pop in his right foot as he ran the bases after hitting a pop fly against the New York Yankees.
Pena originally didn't want to go on the disabled list, preferring to return sometime in the next few days and play through the injury, a slightly torn ligament. The tear cannot be repaired with surgery and is expected to heal on its own.
"I'm not thrilled about it but I'm getting over it," he said of the decision to put him on the DL.
Pena felt better about things after Rays doctors and coaches convinced him to take the extra rest and come back at full strength.
"Would I rather play eight weeks at 75 percent or seven at 100?" Pena said. "For me, that's a no-brainer, I'd rather play seven weeks at 100 percent."
The move also gives Rays manager Joe Maddon an extra reliever.
"These guys have been doing a phenomenal job and if we keep asking them to do too much their effectiveness is going to go away," Maddon said of his bullpen.
Pena, who is batting .212 with 23 homers and 68 RBIs, is eligible to come off the DL on Aug. 16, when the Rays open a three game series at home against the Texas Rangers.
Thayer was 2-1 with a 3.35 ERA and three saves in 37 games at Triple-A. He pitched in 11 games for the Rays last season and earned one save.