Burke was rushed to hospital for a spinal scan after being involved in a collision as he chased his own chip.
Play was held up for 10 minutes as Burke was assessed and stabilized before being taken away by ambulance.
Munster had built an early six-point advantage with two penalty by Burke. He broke the deadlock after Derrick Lee wandered offside - then repeated the dose in the wake of a similar offence by Alan MacDonald.
The home side replied in positive fashion, but could not turn pressure into points. They were also thwarted by the pinpoint positional kicking of Burke.
Then came Burke's injury scare, but his departure could not halt the Munster surge. And they stretched their lead four minutes after the restart when winger Shaun Payne powered over after latching on to a pass from recalled All Black Christian Cullen.
Gunners continued to have the better of the territorial action, but they were unable to breach the tight Munster defence. Twice Lee got to within a couple of paces of the line, only to be stopped in his tracks.