Kelly, regarded as the top prospect in the Padres' Minor League system, allowed two hits and one walk and had two strikeouts in a game won by the Mariners, 4-1.
The game lasted seven innings, as agreed upon by Padres manager Bud Black and Seattle manager Eric Wedge.
The Padres had five singles in the game with the hits coming from Rico Noel, Andy Parrino, Anthony Rizzo, Bobby Kielty and Jason Hagerty.
Designated hitter Kyle Blanks, appearing in his first game-like setting, went 0-for-2 with a walk and two strikeouts.
Blanks had reconstructive elbow surgery last season and is behind the rest of the position players in camp. He won't be ready to break camp at the end of the month.
Padres pitcher Rob Musgrave allowed two earned runs on eight hits. Another reliever, Scott Munter, fared better, allowing one hit over two scoreless innings.