Only about 40 of the 816 Nymex members either abstained or voted against the takeover, The Wall Street Journal reported.
CME Chairman Terry Duffy said Nymex was greeted with applause from shareholders when he announced the deal "received the required approval," the business newspaper said.
"In the end, Nymex really had no other place to go," said Lee Stern, a long-time CME shareholder at the meeting.
Based on CME's closing share price of $336.64 -- a drop of 5.9 percent -- the deal was valued at $8.26 billion. Nymex finished down 2.6% at $79.95.
The deal was a year in the making, with a group of Nymex members dissatisfied with the terms threatening to block it.
"Obviously, when it came down to it, this was a fear-based transaction," said Jan Marks, one of the dissident Nymex members. "A lot of people caved in to fear. Those who didn't are the lions, not the lambs."