Bain Capital LLC and Golden Gate Capital agreed to acquire BMC Software Inc., the company that abandoned a sale last year, for $6.9 billion in the third- largest private-equity deal of 2013.

The buyout investors, which also include GIC Special Investments Pte Ltd. and Insight Venture Partners, agreed to pay $46.25 a share in cash, BMC said in a statement today. Elliott Associates LP, which owns a 9.6 percent stake, will vote in favor of the transaction, BMC said.

BMC held talks last year with buyout firms amid pressure from activist investor Elliott Associates before deciding to buy back $1 billion in shares instead. BMC attracted renewed interest in March stemming from the upcoming expiration of Elliott’s standstill agreement, a person familiar with the situation said at the time.

“The deal makes sense given how much cash flow the company can manage from its mainframe operations,” said Kirk Materne, an analyst at Evercore Partners Inc. in New York. Bain is paying about nine times Materne’s projected 2014 cash flow, “which seems reasonable,” he said.

Shares of BMC fell less than 1 percent to $45.35 at 9:52 a.m. in New York. The software maker had a market value of about $6.5 billion as of May 3.

BMC sells software that manages fleets of computer servers and mainframes, configuring new machines and applying updates to older ones. The company does business in two areas -- a unit that makes software for managing server networks and the other for mainframe products.

Only two private-equity deals announced so far this year are bigger than the proposed BMC transaction -- the sales of HJ Heinz Co. and Dell Inc. BMC’s agreement with Bain includes a 30-day period to solicit alternative proposals, according to the statement.

Elliott is the second-largest shareholder in BMC, according to data compiled by Bloomberg.

“We are very happy with the outcome, which is consistent with our historical approach to value creation in the technology sector,” said Jesse Cohn, a portfolio manager at Elliott.

Technology