Five directors, including chief executive Kevin Hart, were removed at a meeting of shareholders called by Monaco-based private equity firm Crown Ocean Capital (COC).
A resolution calling for the removal of chairman Billy Allan was defeated.
Mr Allan and chief operating officer David Clarkson will keep their posts.
Two nominees put forward by COC - Christopher Ashworth and Eli Chahin - were appointed to the board with immediate effect.
Africa-focused Bowleven said all resolutions proposed at the general meeting would have been defeated "by a significant margin" without votes cast by COC and its nominees.
The board had urged shareholders to vote against the resolutions, arguing they were "not in the interests of all shareholders".
COC had been calling for a change in direction by the company. Among other things, it demanded that Bowleven focus on maximising value from its Etinde interest in Cameroon and not devote any resources to new projects or acquisitions.
Mr Hart joined the Bowleven board in November 2006, having been finance director at Cairn Energy for more than eight years.
Before that, he was a senior associate director with Deutsche Morgan Grenfell Group, specialising in oil and gas sector mergers and acquisitions.
An activist shareholder has succeeded in ousting most of the board of Edinburgh-based oil and gas exploration firm Bowleven.