The home side took the lead inside ten minutes when Xherdan Shaqiri drove a low, powerful ball across goal which was deflected away by David de Gea but only as far as Marcos Streller who hit the rebound into the ground to see it head into the back of the net as United defender Chris Smalling lay injured on the ground from a collision just prior.
United's small uphill battle became a mountain late in the match when Alexander Frei headed home Xherdan Shaqiri's cross from the right which somehow found its way to the back post for the striker to net his fifth group stage goal.
There was a late glimmer of hope for United when Phil Jones forced a header over the line after Federico Macheda fired his shot into the crossbar but the Basel defence stood strong to deny last season's runners-up a chance to redeem themselves in Europe's premier club competition.
United were not without their chances as Wayne Rooney completely miscued his 30th minute attempt from Nani's pinpoint cross before the Portuguese was denied by Basel keeper Yann Sommer five minutes later. Their best chance before the late goal came from a Basel player when Markus Steinhofer attempted to clear Nani's swinging cross but somehow managed to cannon the ball into the crossbar.
Champions League Group C