Thome hit a pinch-hit home run leading off the bottom of the ninth inning to lift the Phillies over the Tampa Bay Rays 7-6 after Papelbon blew his first save chance in 18 tries this season.
Papelbon said he told Thome in the on-deck circle that he would give him $5,000 if he hit a homer. Papelbon said he wrote the check in the clubhouse. Thome, however, told the Philadelphia Inquirer that he hadn't received any payment.
"That was a huge pickup by Jim Thome," Papelbon said. "I couldn't be happier for anybody in the clubhouse."
Papelbon (2-2) allowed his first earned runs in a save situation this season. He walked Jose Lobaton with two outs to extend the game. Jeff Keppinger followed with an RBI single. Then, Brooks Conrad ripped a run-scoring single to right to tie it. Conrad was 3 for 41 before that hit.
"I've got to do a better job," Papelbon said.
"You never forget them," Thome said. "These are moments you never know how long you'll have them."
Information from The Associated Press was used in this report.