Without the option to fine Tesco for the overbuild, the council's planning committee instead insisted the supermarket meet conditions before the store is allowed to stand.
A 6,130 sq ft area, already cordoned off within the store, will be left unused until a future planning application is passed.
And Tesco will pay £788,502 to fund a free town centre circular bus service for the next five years - £125,000 more than previously agreed.
In addition, the committee also determined it necessary for the bus to be "green" and a public art sculpture on the site be protected from rain.
Coun Derek Whitehead added: "I think this is the second most important planning decision made in Stockport. The first was 150 years ago when some bright spark insisted that every train using the viaduct stops in Stockport. We have to find a solution where it's clear we are in control.
As Tesco's retrospective planning application is contrary to Stockport's current Unitary Development Plan the final decision now rests with the secretary of state, Ruth Kelly.
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