The pop legend beat Bruce Springsteen and Roger Waters to the top spot in the chart posted by Billboard.
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The singer's tour grossed a total of $228,406,085 (£141 million), selling out every one of its 72 dates.
Bruce Springsteen and The E Street Band totalled $199,371,791 (£123m), with Pink Floyd founder Waters in third with $186,466,703 (£115m).
Madonna's 'MDNA Tour' saw her booed by French fans for delivering a short set and criticised for wielding a gun on stage following the July Colorado shooting.
'Michael Jackson: The Immortal World Tour' by Cirque du Soleil was the fourth highest-grossing tour of 2012, followed by Coldplay in fifth and Lady GaGa in sixth.
Madonna outsold Lady GaGa by three-to-one in Latin America.
Photo gallery - Madonna's 'MDNA Tour' in Hyde Park:
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