Ackman and Canadian Pacific have been fighting an increasingly acrimonious battle since last fall, when the investor's Pershing Square Capital Management LP announced what is now a 14% stake in the Calgary, Alberta-based railroad.

Pershing Square had nominated seven candidates to CP's board, the first step toward revamping management and installing one-time Canadian National Railway Co. executive Hunter Harrison as CEO.

Momentum had been building for Ackman, who received the backing of three influential proxy advisory services and the endorsement of shareholders Ontario Teachers' Pension Plan and Canada Pension Plan Investment Board. Canadian Pacific said on Thursday morning that CEO Fred Green had resigned along with board chairman John Cleghorn, one-time chairman and CEO of Royal Bank of Canada, and four other directors.

"The board wishes to thank Fred for his dedicated years of service," Cleghorn said in a statement.

Canadian Pacific said that the directors decided to resign "after taking into account the views expressed by shareholders about the desire for board change."

With the resignations, there are only 16 candidates for the 16 board positions, CP said, meaning Ackman and his nominees will be elected to the board.

No CEO replacement for Green was named, but the board was expected to meet following the annual meeting.

Ackman has argued during the proxy contest that CP's stock has trailed its peers because the company mishandled its capital and was slow to extract efficiencies from its operations.

The investor, speaking at the meeting, told investors, "We hear loud and clear your mandate for change" but warned it would not happen overnight.

But the outcome of the meeting did persuade at least one analyst, Barclays Capital's Brandon Oglenski, to upgrade Canadian Pacific stock and raise his price target for the company.

Oglenski said in a note that he expects the management change to produce "a revitalized operational focus from the ground up" that "will drive meaningful improvement over the near-term."