Andrea Stella, who moved with double world champion and Le Mans victor Fernando Alonso from Ferrari to the British-based team in 2015, was appointed performance director, responsible for trackside operations.
Boullier had effectively run the team since he arrived at McLaren in 2014 but a restructuring in April left him reporting to Brown, an American marketing expert brought in after former boss Ron Dennis was sidelined. Boullier, 44, insisted only a fortnight ago that he would not resign despite reports of a staff revolt at the team's Woking headquarters.
"Ultimately, he wants what's best for McLaren as we all do, so when he ultimately made his decision it was not a surprise. It was something we had spoken about in our challenges and potential ways to address them".
McLaren have won 20 drivers' and constructors' championships, but they are without a victory since 2012, and have failed to finish on the podium in more than four years.
Their boast previous year that they had one of the best chassis has been undermined by a continuing lack of performance while Red Bull, who use the same engine, have won three races. Stella had joined McLaren with Fernando Alonso from Ferrari.
Zak Brown, the team's American chief executive, said the staff were not to blame and Boullier had to go because of the failure of this season's auto - they have just 44 points and are sixth in the constructor's championship.
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McLaren is sixth in the constructors' championship, 203 points behind leader Ferrari.
"Obviously our results this year have demonstrated that we have a big performance issue", Brown said in a media call today.
"We have done a lot of work behind the scenes and we are now taking measures to rebuild McLaren and to make us a race-winning organisation". De Ferran has continued to remain close to Alonso and also Zak Brown.
Being the second most successful team in Formula One, the team in its present-day has lost direction which has resulted in the fans losing their optimism of seeing the papaya orange vehicle fighting for podiums if not championships.
"It is an unacceptable situation that we find ourselves in, and it is a very painful situation but the one thing we will not do is quit".
McLaren chief executive Zak Brown says the team's performance this year "has not met the expectations of anyone at McLaren" and that "the causes are systemic and structural, which require major change from within".