Counting of votes will take place on Thursday.
Aurangabad has 113 wards, however two Shiv Sena candidates -- in wards 100 and 103 -- had already been elected unopposed.
Shiv Sena and BJP contested in an alliance in both municipal corporations while the Congress and NCP contested separately.
Sena is in power in Aurangabad for the last 30 years whereas Navi Mumbai, a satellite town of Mumbai, is known to be a stronghold of NCP leader Ganesh Naik.
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State BJP chief Raosaheb Danve however said that BJP- Shiv Sena alliance will win in Aurangabad.
In Aurangabad, a total of 8,95,940 voters (Male-4,30,635, female- 3,85,305) cast votes. There were minor incidents of stone-pelting and scuffles.
Elsewhere, the voting percentages in civic polls were as follows: Ambernath municipal council: 48.81 percent, Kulgaon-Badlapur municipal council: 59 percent, Rajgurunagar (Pune): 72 per cent, Varangaon (Jalgaon): 77.23 per cent, Bhokar (Nanded): 74.4 per cent, Movad (Nagpur): 87.90 per cent and Wadi (Nagpur) municipal council: 62.3 per cent.
"Counting will start at 10 am on Thursday and the election code of conduct will be over once all the results are declared," said the state election commissioner.