Dunn, 34, died early Monday in a fiery car crash in suburban Philadelphia. Police say speed may have been a factor in the crash.
Referring to a photograph Dunn had posted on Twitter early Monday in which he is seen drinking with friends just hours before the 3 a.m. accident, Ebert tweeted: "Friends don't let jackasses drink and drive." The photo has since been removed.
Ebert later wrote in a Tuesday blog post, "I was probably too quick to tweet. That was unseemly."
The tweet from Ebert, a prolific user of Facebook and Twitter, prompted a landslide of posts, some profane, criticizing Ebert on his Facebook page.
"Jackass" co-star Bam Margera tweeted that Ebert's response to the tragedy was insensitive.
"I just lost my best friend, I have been crying hysterical for a full day," he said in a pair of angry, obscene messages.
Ebert responded, asking Facebook in a tweet: "Facebook! My page is harmless and an asset to you. Why did you remove it in response to anonymous jerks? Makes you look bad."
A few hours later Ebert tweeted that his Facebook page was back online.
Ebert wrote in a Tuesday blog post that he wasn't calling Dunn a jackass. Instead, Ebert said he was referring to Dunn's association with the multimillion-dollar "Jackass" TV and movie franchise.
"It was not intended as cruel," Ebert wrote. "It was intended as true."