Shell will also not be able to prevent competitors from using its liquefaction facilities that supply LNG into the European Economic Area (EEA) or from its gas transportation and processing infrastructure in the North Sea, the Commission said in a statement.
The Commission's investigation focused on the markets where the activities of the two companies overlap, it said: in exploration for oil and gas reserves and in the supply of natural gas and liquefaction and supply of LNG.
The merged entities' market share in these areas will remain small, it said, and a number of strong competitors will remain active. The takeover will not allow Shell to influence prices, the Commission said.
The merged company will also be unlikely to stop competitors using its infrastructure, because "significant additional liquefaction capability" is being built and will be available in the near future, and "significant" spare capacity already exists, the Commission said.
Shell chief executive Ben van Beurden said: "Receiving clearance from the European Commission underlines the good progress we are making on the deal. The transaction is on track for completion in early 2016. The recommended combination with BG is a springboard to change Shell into a simpler and more profitable company, making Shell more resilient in a world where oil prices could remain low for some time."