The Padres' top prospect struck out four and allowed one hit over five shutout innings Friday before Double-A San Antonio posted a 2-1, 14-inning triumph over Springfield.
Kelly, recovering from a strained right elbow ligament, walked one and faced one batter over the minimum for the Missions. He retired the first six Cardinals before giving up a leadoff double to Adam Melker in the third.
"This was probably my fourth outing back and I just wanted to go out there and command my fastball," Kelly said. "Obviously, as the game went on I started throwing more off-speed pitches. I felt like my fastball command was the best since my comeback."
Kelly, who was long gone by the time pitcher Robert Lara delivered a walk-off single, began the year with Tucson. He yielded three earned runs in two starts for the Triple-A Padres but missed 3 1/2 months before making three rehab starts in the Rookie-level Arizona League.
"It was good to be out there and obviously, in the Texas League you're facing a lot of good hitters," Kelly said. "It's good to get back in the game mode and see some different hitters."
Kelly spent all of last season with San Antonio, going 11-6 with a 3.98 ERA in 27 starts. In his final start last year, the 22-year-old right-hander limited Midland to one hit over five innings.
"I liked pitching in the Texas League last year and I love pitching in San Antonio, it's a pitcher's park," he said. "You gotta love pitching in those parks."
Kelly said he was limited to 70-75 pitches on Friday and was unsure what his next step will be, although he's not too concerned.
"I'm just trying to take it day by day and make sure the elbow feels good after the start," he said.
Dustin Pease (3-2) got the win, allowing two hits over two innings.
The Missions loaded the bases with two outs in the 14th for Lara, who was hitless in four plate appearances since he was promoted from Class A Advanced Lake Elsinore. But he batted for Pease and stroked a line drive to right field to end the game after four hours and 42 minutes.
Michael Blazek (5-6) allowed a run on three hits while retiring two batters for Springfield. Starter Carlos Martinez, the Cardinals' No. 2 prospect, allowed a run on four hits over five innings.