The vote makes Pixar a wholly owned subsidiary of Disney and makes Pixar Chief Executive Steve Jobs Disney's single largest shareholder with about a 7 percent stake.
The deal is squarely aimed at restoring Disney's luster as a leader in the animated film business. Disney's own efforts have faltered over the past 10 years while Pixar's films have been huge successes.
Jobs, who will be named to Disney's board, had already said he would cast his Pixar shares, which represents 40 percent of the company's outstanding stock, in favor of the merger. Shareholders met briefly in San Francisco Friday to ratify the deal.
After the vote, Disney filed a registration statement for the stock it will use to finance the deal. Under the plan, Pixar shareholders will exchange each of their shares for 2.3 shares of Disney stock.
The acquisition was expected to close later Friday.
The deal comes just a month before the partnership between the two companies was set to expire.
Disney agreed to finance the first computer-animated feature film, "Toy Story," in 1991. The film was released in 1995, the same year Pixar became a public company.
The relationship between the two companies has produced a string of box-office hits, including the films "Finding Nemo" and "The Incredibles." The seventh and last film under the old distribution agreement, "Cars," will be released June 9.
Talks to extend the agreement began two years ago, but faltered in large part because of personal animosity between Jobs and former Disney CEO Michael Eisner. Talks resumed after Robert Iger was named to succeed Eisner as CEO last year.
Those talks graduated to discussions about an acquisition after Iger saw research that showed mothers with children under the age of 12 rated the Pixar brand ahead of Disney.
Iger told analysts in February that he became convinced Disney should buy Pixar after presiding over the opening of Hong Kong Disneyland last September.
"I was at the opening of Hong Kong Disneyland and standing with a few thousand other people watching the parade go by and I realized that there wasn't a character in the parade that had come from a Disney animated film in the last 10 years except for Pixar," Iger said.
"It really hit me hard that we had had 10 years of real failure in many respects in the business that I believe was the most vital to us."