And for that, they still won, salvaging a game in the three-game series before a crowd of 17,923 at Petco Park -- fans who probably had trouble digesting what they were seeing.
Not Kennedy, though, as he lowered his season ERA to 3.39 by allowing two runs over six innings, as he also won for the fifth time this season.
One hit, one fly ball, Kennedy could care less. The right-handed pitcher had his eye on only one number.
"The important part of the column is the runs column," he said.
This marked just the third time in franchise history the Padres won a game with one hit. The other two games occurred on July 19, 1975, against the Cubs and April 20, 2010, against the Giants.
This was the second time this season a team has won with one hit. The A's topped the Rays, 3-2, on May 21.
"There's a lot of ways to win a baseball game and that was one of them. You never know what's going to happen in a big league game. The game starts, you never know how it's going to unfold," said San Diego manager Bud Black.
"When you win a game like that and only have one knock, it's a pretty good win."
The Padres (27-33), who are off Thursday, didn't need a lot of hits to edge the Pirates (28-31), not as starting pitcher Francisco Liriano (1-6) didn't give them much to swing at.
Liriano walked six over five innings, allowing the bunt single to Everth Cabrera, and two earned runs. He also had seven strikeouts.
"We had him on the ropes a couple different times and couldn't get the big knock," Black said.
Luckily, the Padres got a little one -- about the smallest you can get, as Cabrera dropped down a bunt for a hit in the bottom of the first inning, which helped set up the first run of the game.
"We don't hit that much and if I have the opportunity to do that, I'll do it 100 times," Cabrera said.
The Padres first run came in that first inning when Carlos Quentin lifted a short popup into shallow right field, as second baseman Josh Harrison drifted back and made the catch. Chris Denorfia tagged up from third base and scored as Harrison's throw was up the line.
A second run in the inning scored when Tommy Medica's bouncer back to Liriano eventually turned into a throwing error by Harrison who tried to complete a double play.
Liriano's wildness played a big role in the Padres' third run of the game, as he walked four in the fourth inning. The last walk, to Denorfia with the bases loaded, forced a run.
"That was a weird one for me," Liriano said. "Too many walks, getting behind the count too much. Just wasn't executing pitches. I didn't have rhythm anywhere."
Kennedy (5-6) didn't have any such problems, as he threw a lot of strikes early, got a lot of balls in play early in counts and got a lot of mileage out of his curveball.
"Ian pitched well. The last three or four starts he's been pretty darn good. Today, the fastball command, the hook, the change. All three pitches working," Black said.
Kennedy allowed a home run to Andrew McCutchen in the third inning and an RBI double to Harrison in the fourth inning but little else. He allowed five hits in six innings with one walk and seven strikeouts.
Kennedy heaped a lot of praise on Rivera, who has fast become a favorite of the pitchers on the staff to work with.
"I think I've shook him only five times in the last three starts," Kennedy said. "… And when I gave up the home run, he was madder than I was."
Kennedy came out of the game after only 88 pitches as the Padres had a chance to score more in the sixth inning. But Seth Smith grounded into a double play to end the inning.
The Padres' bullpen took care of the rest as Nick Vincent, Joaquin Benoit and closer Huston Street got the final 12 outs of the game, with Street working a scoreless ninth inning for his 18th save.
"If you look at what they've done so far statistically, it's been outstanding," Black said of the bullpen. "If you look at the games that we've won, they've been a big part of that. Most of our wins come with low-scoring games, so we have to pitch well. So they're doing their part big-time.
"At the end of the game those outs are tough."