Membership was approved by 237 votes to 54 but only after a lengthy delay as delegates struggled to reach a deal on Wednesday.
Muslim countries raised legal and procedural concerns to challenge a December pact that had cleared the way for the entry for Israel's Magen David Adom and the Palestine Red Crescent.
Tunisia and Pakistan proposed changing the deal to identify occupied lands, including East Jerusalem and the Golan Heights, as under the jurisdiction of their respective Arab relief societies - an amendment Israel would not accept.
The advocacy group UN Watch said representatives from Saudi Arabia and Iran were among those who criticised Magen David Adom and sought to hold up its admission during the session.
"It is tragic that a conference with purely humanitarian purposes should be put at risk by politics and rhetorical point scoring," Hillel Neuer, UN Watch executive director, said.
Magen David Adom has sought membership in the Red Cross movement since the 1930s - even before Israel became a state - but had been barred because it objects to using the traditional symbols of the movement to identify its medical and humanitarian workers.
The addition of a third emblem to the red cross and red crescent had paved the way for Israel to join the organisation.
The red crystal - a red-bordered square standing on its point - was endorsed in December but needed to be approved at the conference.
The red crystal will be used on Magen David Adom ambulances and by other agencies in areas where the neutral symbol seems more appropriate.
Palestine Red Crescent had previously been excluded from the movement because only sovereign nations are represented. The meeting dropped that requirement in the case of the Palestinian Authority.
Mohammed Al Hadid, the conference chairman, said the move should result in better co-operation between Israeli and Palestinian relief services, and ensure more universal access to those needing help from the agency.
The original Red Cross symbol - a reversal of the colours on the Swiss flag - was adopted in the 1860s when the organisation was set up to care for wounded soldiers.
Muslim nations objected to the use of the cross, which they said reminded them of the Christian crusaders, and adopted the Red Crescent symbol.