Soto was credited with an inside-the-park three-run homer in the fourth inning despite replays showing that it should have been an automatic home run in Chicago's 7-2 win over Houston on Monday night.
The ball bounced just to the right of the yellow line on the wall in left-center field.
"It was a home run, but I think he'd probably rather have the inside-the-park home run anyway," Piniella said.
Astros center fielder Michael Bourn scooped it up and threw it home, but Soto scored easily before the throw got there.
"Never in my whole life had I had an inside-the-park home run," Soto said. "I didn't think it was out. It's so big that left-center area I didn't think I hit it over it. I thought double, maybe triple if they misplayed it."
Third-base umpire Ed Rapuano defended his call.
"The ball hit the yellow line that designates home run, no home run," he said.
When asked if there was any question in his mind when he made the call, he said: "No. I called what I saw."
It was the second consecutive night that major league umpires botched a home run call. New York Mets first baseman Carlos Delgado was robbed of a three-run homer Sunday night. Delgado's ball was originally ruled a home run but the call was reversed, turning it into a long foul ball. The replay of that play showed it should have been a home run.
Delgado ended up with an RBI single.
Soto's was the first inside-the-park home run for a catcher since Joe Mauer of the Twins hit one against the Angels on July 21 according to the Elias Sports Bureau. The last National League catcher to achieve the feat was Kelly Stinnett for Arizona on Aug. 29, 2005.
It's been almost 49 years since a Cubs catcher hit an inside-the-park homer, dating back to Cal Neeman's hit on June 17, 1959 against Pittsburgh's Harvey Haddix.
It's the first one for the Cubs since Derrek Lee hit one on Aug. 26 and the third in Minute Maid Park history.
The win is Chicago's ninth in the last 11 and puts the Cubs at 11 games over .500 for the first time since finishing the 2004 season at 16 over.
Astros starter Brian Moehler (1-1) allowed seven hits and three runs in five innings.
Ted Lilly (5-4) allowed four hits and two runs with six strikeouts in 5 1/3 innings for his fourth consecutive win. He didn't allow a hit until a double by Miguel Tejada with one out in the fourth inning.
"What a great play, going up that hill, keeping your balance, keeping your concentration and gloving it," Piniella said. "That's as fine a play as a center fielder can make."
Theriot had a run-scoring single in the eighth inning to make it 5-2.
The Cubs were able to shut down Houston's hottest hitters on Monday, breaking Lance Berkman's 17-game hitting streak and the career-high 16-game one by Pence. Both were 0-for-4 and Berkman struck out three times.
Chicago's Mark DeRosa tallied two hits on Monday to extend his hitting streak to 10 games, leaving him just one shy of his career mark.
The Astros had a chance to cut the lead in the eighth. Bourn singled before stealing second base. Kazuo Matsui followed with a single that sailed just over the glove of a leaping Derrek Lee.
Marmol pitched out of trouble with three consecutive outs. Tejada popped out, Berkman struck out swinging and Carlos Lee was out at first.
"Marmol did a heck of a job, but he's been doing that all year," Piniella said. "He was outstanding."
- Astros ace Roy Oswalt, who left his last start in the seventh inning with a hip injury, was examined by team physician Dr. David Lintner on Monday and is expected to make his next start on Thursday.
- The Cubs placed RHP Chad Fox on the 15-day disabled list on Monday night after he experienced numbness in his hand throwing before the game. Jose Ascanio was called up from Triple-A Iowa to take his place on the roster.