Egyptian champions Ahly were close to losing the league game to their arch rivals but Barakat hit a last-ditch stunner to end the match in a thrilling 3-3 draw.
Some replays and photos showed that the 33-year-old actually gave Zamalek's fans the finger.
However, the Egypt ace assured that he didn't cross the line by any means while celebrating his goal.
"Everybody knows me, I would never do that," Barakat told Dream TV.
"I have been playing (professional) football for 15 years and no way would I make this kind of gestures.
"After I scored I ran towards Al-Ahly's supporters, so this allegation doesn't make sense.
"All I did was raising my hand up. I always do that while celebrating."
Zamalek are filing a complaint against Barakat, according to club spokesman Sabri Serag.