The short answer is no, GMAT won't act as a substitute for University grades.
A Good GMAT score could be helpful though in some cases, for example:
1) If you are doing a non-quantitative degree, a good GMAT quant score can demonstrate your quantiative ability
2) If you are studying at a University where the scoring system is not easily understood by the office you are applying to, then GMAT could serve as a decent benchmark.
A 3.6 GPA by no means would be an application killer, so I wouldn't worry too much at this point, and work on the other parts of your CV (e.g. extra curriculars, getting more work experience) and on pushing up your GPA with the courses you have left.
Hope that helps!