The range is to be released in fall 2008 and will be retailed exclusively in physicians' offices in the US.
The collaboration represents a further blurring of boundaries between medical and cosmetic sectors as increasing numbers of products with surgery inspired marketing and ingredients hit the market.
Products in the range will be targeted to complement non-surgical cosmetics procedures such as laser treatment, dermal fillers, botox injections and microdermabrasion.
Physician-dispensed skin care is a growing retail channel in the sector and Allergan hopes to lead the way with the range.
Although sales remain small they are growing at a double digit rate, Allergan told the Wall Street Journal.
"In collaboration with Clinique, our goal is to establish a leadership position in physician-dispensed skin care…" said Allergan CEO David Pyott.
According to the company, increasing numbers of consumers are undergoing cosmetic procedures and seeking advice and treatments from cosmetic physicians.
By placing the line for sale in doctors' offices the company hopes to benefit from the growing number of consumers who wish to buy their skin care products from trusted specialists.
Clinique says the agreement reflects the company's dermatological heritage.
"This new skin care line, created in collaboration with Allergan, is the next generation of the expression of Clinique's unique position delivered through one of the fastest growing channels today, the physicians' offices," said Estee Lauder Companies CEO William P Lauder.
The line is to be formulated, developed and manufactured by Clinique while Allergan will take care of marketing and distribution.
However, the two companies have said they may work together to conduct clinical trials of the products and work with the physician community to promote the products.
Products that take inspiration from cosmetics procedures are becoming increasingly prevalent in the anti-aging sector.
Product names that play on the botox theme are popular such as UK brand Glamotox and Medic8's Pretox range.
Many such products contain neuropeptides, which work to inhibit muscle contractions and therefore skin wrinkles in a similar way to botox injections.