The two pharmaceutical manufacturers will together contribute half the funding for a 150 million euros (125.3 pounds) fund being launched by Index to invest in early-stage life sciences projects, primarily in Europe.
The three-way collaboration aims to capitalise on Index's successful track record in backing companies with just one or two projects - a so-called asset-centric approach that has already led to a number of trade sales and flotations.
Deals such as the sale of PanGenetics, an Index-backed firm, to Abbott Laboratories
This is a completely new collaboration model, Index partner Francesco De Rubertis said in a telephone interview from Amsterdam, where the three partners will explain their strategy at a biotech conference later on Wednesday.
It is really a bet by GSK and J&J on the new investing model that Index has developed over the last five years or so.
Under the deal, Index's existing limited partners will put up the other half of the cash and the venture capital (VC) firm will maintain full decision-making rights to the portfolio of companies in which it invests.
That means GSK and J&J will have no preferential rights to acquire any promising new drugs emerging from the investment, although they will get an inside view.
The VC fund's scientific advisory board will include four representatives from the drug companies - including Moncef Slaoui, GSK's chairman of research and development, and Paul Stoffels, J&J's chairman of pharmaceuticals. They will sit alongside five Index-appointed executives.
The deal reflects a new willingness among some of the drug industry's biggest names to consider sharing early research efforts as times get tougher.
Faced with a wave of patent expires, pressure on new drug prices and poor investment returns on their R&D dollars, large drugmakers are eager to consider different ways of tapping into the best science.
Slaoui said the Index initiative was an example of GSK being creative in nurturing the biotech ecosystem, while J&J's Stoffels said it should improve the chances of identifying early-stage technologies in key disease areas.
Five to 10 years ago it would have been more difficult to do this, but pharma productivity in R&D has gone down and so pharma companies are trying new approaches, De Robertis said.
Other novel approaches to R&D being considered by drug companies include pooling some early-stage research before it reaches a competitive phase - a concept with parallels to the open-source notion in computing which created Linux software.
($1 = 0.7552 euros)
(Editing by David Holmes)