The resignation of the leading executive comes weeks after the company announced that Proctor and Gamble (P&G) executive Fabrizo Freda would become chief operating officer from March next year.
The company announced the resignation of Shearer in an SEC filing stating that the group president's departure was effective immediately.
Shearer joined the company in 2001 as president of its international division and took charge of sales and profits outside the US.
The senior executive then became group president in 2003 and now leaves his current role as head of the Clinique, Aveda, Origins, Bumble and Bumble and Ojan brands.
His senior position also made him responsible for Estee Lauder's online business.
"Philip has done a wonderful job over the past six years," said Estee Lauder CEO William Lauder. "He has been a strong contributor to our company's leadership."
Employees who reported to Shearer will now report to Lauder until the arrival of incoming president and chief operating officer Fabrizio Freda.
Lauder revealed at the company's annual general meeting this month that he expects Fabrizio, who was previously head of global snacks at P&G, to succeed him as CEO within 24 months.
The company recently announced a 4.9 percent growth in its first quarter sales, which came in at $1.71bn, but said that net profits for the period fell by 27 per ent to $77.9m, mainly as a result of the poor performance in the mainstay US market.