Some felt the scene, in which Rhona Goskirk was raped by Pierce Harris just hours after their wedding, was not suitable for broadcast before 21:00.
But the media watchdog said the scene "was likely to have been in line with what most viewers were expecting".
"We took into account the broadcaster had issued a warning and the scene was limited," it said in a statement.
"Emmerdale is known to have covered many challenging social issues."
The scene, shown on 24 April, was the culmination of a long-running storyline involving Rhona, played by Zoe Henry, and her abusive partner Pierce, played by Jonathan Wrather.
"I know some have said it's too much for a 1900 time slot," Emmerdale producer Iain MacLeod told Metro after the episode was broadcast.
"My response to that is Emmerdale has always covered hard-hitting subjects and I think soap has a responsibility to cover them."
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A harrowing rape scene from ITV soap Emmerdale will not face an Ofcom probe despite generating 101 complaints.