The Egypt international, who was on the bench for Tuesday's game, was incensed after Al Ahly's appeal for a penalty following a handball in stoppage time was denied.
"He handed a four‑match ban and fined 50,000 Egyptian pounds ($942) for assaulting the referee by pushing or pulling (use of the hand without violence)," the league said in a statement.
The ban means El-Shenawy, who is expected to be Egypt's starting goalkeeper at the World Cup in North America, will be sidelined until the final week of the league play-offs.
Al-Ahly are third on 41 points, five points behind leaders Zamalek.