Jonathan Lopez, a Brooklyn sixth-grader in a schoolyard tussle with two girls, got caught up in the sex-harassment tornado.

Jonathan insists he only tried to grab the water bottle and backpack of classmates who had tossed his stuff during lunchtime horseplay.

But the school charged him with “conduct of a sexual nature.” He was accused of trying to touch one girl’s breast and kiss her and of “humping” another girl from behind.

“Like, I’m not sexual,” the baby-faced 11-year-old wrote in a city Department of Education statement. “I do dumb thing [sic] but I’m not sexual to girls.”

The dean at MS 88 in Park Slope pressured him to admit lewd behavior or plead “no contest” and waive his right to a hearing, Jonathan told The Post.

“After what you did, I don’t want to see you in my school,” he said the dean, John Roumbeas, told him.

Jonathan refused. “I told him ‘I’m not going to admit to it because I didn’t do it.’ ”

That day, the school banished Jonathan to a distant suspension center, populated by tough older kids who “bring knives,” he said. “They roamed around the halls and didn’t listen to the teacher.”

In the end, a suspension judge found no evidence of breast-touching, kissing or humping and ordered Jonathan’s “immediate reinstatement.”

But he missed 16 days of classes.

“They treated him like a criminal,” fumed his dad, Mahoma Lopez.

The tsunami of sex-harassment allegations in the news “escalated things” against his prepubescent son, Lopez suspects.

“They’re real predators,” he said of Harvey Weinstein and other offenders. “The school is making an example of my son. He’s an innocent kid who just wants to play.”

Maria Chickedantz, a feminist lawyer who has known Jonathan since he was 6 and took up his case, described him as sweet and friendly. “The kid hasn’t even hit puberty yet. He’s little and immature,” Chickedantz said.

Jonathan’s troubles started on Nov. 22, when a girl classmate complained that Jonathan had harassed her.

“He comes up to me (2 inches away) and pretends to sqush [sic] my chest. Then he runs away. I chase him to tell him to stop,” her written statement says. “After he takes my water bottle and I have to chase him up and down and I chased him for 10 minutes. And he said, ‘You should be my girlfriend. We can forget about what happened’ ” and he leaned in and tryed [sic] to kiss me. And he was about 1 foot away.”

She said Jonathan had harassed her friend days earlier. That girl gave a statement: “I was walking with my friends when Jonathan comes out of no were [sic] and he lifts up my bag and he is touching my back and he starts humping me. I tell him to stop but he keeps doing it four more times. He humped me one last time and I almost fall down the stairs.”

The Dec. 13 hearing was a bust. Roumbeas, the dean, did not show up, so the statements he took were not admitted as evidence.

The first girl who accused Jonathan also did not show. The second girl testified that Jonathan grabbed her waist but she never mentioned “humping.”

Hearing officer Anthony Jordan sustained a sole charge that Jonathan “placed his hands” on the girl’s waist. He ordered that records of the matter be expunged at the school year’s end.

But Jonathan was still treated like a sex offender. On his first day back, the dean warned he was “in more trouble” for not confessing, Chickedantz wrote in an e-mail to Principal Ailene Altman Mitchell.

“Faculty, staff and students now see him as some sort of sexual predator, which is so unfair,” Chickedantz wrote. “Even if the accusations were true, the manner in which the school . . . treated an 11-year old like a dangerous criminal was absolutely unacceptable.”

Mitchell and Roumbeas did not return messages. DOE spokeswoman Miranda Barbot said, “The school followed protocol in reporting, investigating and addressing these incidents.”