HONG KONG (Reuters) - China Vanke, the mainland's biggest property company by sales, said it will acquire a unit of Shenzhen Metro Group for 45.6 billion yuan ($6.9 billion) via a new share issue, making the state-owned subway operator its largest shareholder.

The final purchase price came at the lower end of the 40 billion yuan to 60 billion yuan guidance under a preliminary accord in March as Vanke's management fought to retain control of the company in a battle with its major shareholder, financial conglomerate Baoneng.

Vanke said in a statement to the Shenzhen Stock Exchange late on Friday that Shenzhen Metro will hold 20.65 percent of its enlarged issued share capital upon deal completion, surpassing Baoneng's 19.27 percent after dilution.

According to the deal, Vanke will issue Shenzhen Metro close to 2.9 billion A shares at 15.88 yuan each, representing a 35 percent discount to its last trading price of 24.43 yuan on Dec. 18, in exchange for SZMC Qianhai International Development Co, which owns large-scale projects atop metro facilities in Shenzhen.

"Provision of integrated services surrounding metro facilities will become the most important development direction of Vanke," said company secretary to the board Zhu Xu.

The deal with Shenzhen Metro did not have unanimous support from Vanke's board, however, with three 'no' votes from its current second largest shareholder, state-owned China Resources Group, out of 10 total board seats.

China Resources' directors opposed to pay for the deal through a new share issue, rather than cash, according to Vanke's statement.

China Resources, which currently owns a 15.3 percent stake in Vanke before dilution, criticized the manner in which the property developer struck the deal soon after it was announced in March. Chairman Fu Yuning said the agreement had not been discussed by the property developer's board, calling it "unfortunate".

Vanke's shares have been suspended on the Shenzhen bourse since Dec. 18. Its shares in Hong Kong closed up 3.4 percent at HK$17.52 on Friday.

(Reporting by Clare Jim; Editing by Kim Coghill)