The quarterback passed for 254 yards, and rushed for a further 89 from 14 carries, but was unable to prevent defeat as the Jags mounted a late comeback to win at TIAA Bank Field.
Jackson subsequently posted and then deleted a response on Twitter to a fan criticising him following his side's defeat, one which included an apparent homophobic reference.
Speaking on Monday, Harbaugh revealed he has discussed the issue with Jackson, and while he did not condone his player's actions, defended his reputation.
"[I] just beg guys to not to get into the Twitter world right after the game, especially after a loss," he said. "It's never going to be positive. It's not going be a nice place, you know?
"That's kind of reflected in Lamar's response because... that's not the way he speaks. It's not the way he talks. It's not the words he ever uses. I've never heard him say things like that before."
Harbaugh suggested Jackson may have been pulled into his online dispute, and spoke of the player's character in his defence.
"Lamar Jackson, you've been around him," he added. "He's got one of the biggest hearts of anybody I know. You all have seen him the way he treats people, the way he treats kids, the way he treats the media.
"You get trapped sometimes by someone that's baiting you just a little bit. You can't live there. I think that's not a place he wants to be and that's certainly not things that he wants to say."