The incident happened in the second half of Orient's 3-1 win at Swindon Town on Saturday, a result that took Slade's men back to the summit of League One.
But the 53-year-old was saddened that the victory was marred by an unsavoury incident in which a supporter emerged from one of the home sections to throw punches at Jones.
Slade called for the fan to be banned for life.
"It's a great win but it was clouded in my opinion really by the fan coming on the pitch and throwing three punches at my goalkeeper," Slade said.
"I mean that's absolutely outrageous, that's the worst scene I've seen since I've been a manager at my football club, that's an unbelievable scene.
"He's (Jones) okay, but I mean it doesn't make it right does it, that he's okay? I mean, it's outrageous.
"The supporter, he needs a ban for life, he should never go to another football match."
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