"We have to make sure we're focused and locked in during the game," Ross said afterward. "Sometimes our frustrations can distract us a little bit."
Baez said he was "surprised" when he was pulled but accepted the punishment.
"I never want to be out of the lineup," he said. "I respect his decision. He told me why it happened, and I said, 'OK, it's your decision.'"
Baez, 28, was on first base with one out when Anthony Rizzo hit a fly ball to left fielder Eddie Rosario. The Cubs shortstop was rounding second and headed to third base as Rosario caught the ball, easily getting it back into the infield to double off Baez.
"I lost the outs," Baez said. "I [thought] the whole time that it was two outs. I ran like it was two outs."
After Baez came off the field, cameras caught him and Ross talking in the dugout before Baez headed toward the clubhouse.Sergio Alcantara took over for him at shortstop.
"We had a good conversation, and I think that's behind us," Ross said. "Javy is really important for this team, and he's a leader on this team.
"When you see somebody that might be a little distracted, you try to get somebody else in there that is maybe focused and give that other person a break."
Baez said he wasn't distracted but simply made a mistake.
The Cubs lead the National League in outs made on the basepaths, an area of the game they have had issues in for years. It's the second time in two seasons Ross has benched a former teammate of his from his playing days after pulling Kyle Schwarber for a lackadaisical effort in left field.
"I'm not trying to set an example of Javy, ever," Ross said. "That guy plays his butt off and brings it 99.9% of the time.
"I did not feel good taking Javy out of the game. I never feel comfortable doing that at all. It was in my stomach the entire game."
Baez also indicated the incident was behind them while hoping to turn the page.
"There are no hard feelings," Baez said. "We talked after the game. We're on the same page right now. Things happen. Things happen between teammates and managers. It happens."
The Cubs are averaging 1.8 runs over their past eight games. They are 2-6 in those contests.
Javier Baez benched after mental lapse ends inning
Cubs manager David Ross has a teaching moment with Javier Baez after the star shortstop didn't know how many outs there were to end the fourth inning.