Alinta shareholders on Friday voted in Perth on the deal with 96.1 million proxy votes in favour and 509,000 against.
Earlier on the day, AGL shareholders voted in Sydney with 137.07 million votes in favour and 1.14 million against.
The deal will see AGL merge its infrastructure business with Alinta and subsequently demerge the AGL energy business.
It will create Australia’s biggest integrated energy company, to be named New AGL, with $14 billion in assets under management.
It will also establish the nation’s largest energy infrastructure company, to be called New Alinta, which AGL shareholders will own about 44%.
AGL chairman Mark Johnson said the merger would improve shareholder returns by 15% annually.
“This decision positions AGL shareholders for continued growth in returns as they share in the future expansion of both new AGL and new Alinta,” he said.
Johnson said costs associated with carrying out the merger would reach $102.1 million.
Both companies said they would have to slash jobs as they integrate.
Meanwhile, the Australian Competition and Consumer Commission today rejected a proposal of varied undertakings by Alinta that would allow it to take over Australian Pipeline Trust.
“The ACCC will not accept the current offer of a varied undertaking from Alinta,” ACCC chairman Graeme Samuel said.
“The ACCC has significant concerns in relation to the structure and enforceability of the varied undertaking as it currently stands.
“The ACCC is now waiting for Alinta to respond. The ACCC notes that Alinta may engage in further undertaking negotiations.”
Perth-based Alinta currently holds a 10.25% interest in APT and will inherit a further 30% following its proposed merger with AGL.
It was seeking to buy enough of APT to gain control of the company.
The ACCC said that Alinta must sell all of its APT stake within a year of the AGL-Alinta merger’s approval by shareholders.
That undertaking remains in force.
The ACCC said if Alinta were to gain control of APT, it would obtain unacceptable market power in Sydney and Perth.
Alinta, which operates over 20,000km of gas pipes and 12,000km of electricity lines in WA and Victoria, presented the competition watchdog with a new proposal for a possible takeover of APT.
It had indicated that if it were to gain control of APT, it would dispose of pipeline assets such as the Moomba-Sydney Pipeline, Parmelia Pipeline and GasNet Australia Group, to satisfy the ACCC.
Meanwhile, APT today said it now holds a direct majority stake of 50.06% and a relevant interest of 56.51% in GasNet as a result of its unconditional $452 million cash takeover offer.
The offer, of $3.10 per security, is due to close on October 18, unless extended.
APT said it expects to discuss the composition of the GasNet board with its directors next week.