Kelly is San Diego's top-ranked prospect and one of the key parts in the 2010 trade that sent Adrian Gonzalez to Boston. The 22-year-old, who will take Jason Marquis' spot in the rotation, has been bothered by a strained right elbow, but is healthy now.
Thayer missed this weekend's series against Arizona after the birth of his third child with wife, Lisa. The right-hander is 2-2 with seven saves and a 3.89 ERA in a career-high 45 appearances.
The Padres beat the Diamondbacks 5-4 on Sunday for their seventh consecutive win.