The BJP-Shiv Sena combine was ahead in 41 of the 48 Lok Sabha constituencies in Maharashtra, as per trends and results declared till 11.50 pm Thursday.
While the BJP won 12 and was leading in 11 seats, the Sena won 10 and was leading in eight seats, poll officials said.
The ruling alliance had secured 42 seats in 2014 elections.
The Congress, which won two seats in 2014, suffered a setback, losing the Nanded seat and was leading in Chandrapur.
The AIMIM was all set to have its first MP from the state as its nominee was on the verge of winning a keenly fought election in Aurangabad.
The NCP has won three seats and was ahead in one seat. An Independent also won the poll.
The winners include senior BJP leaders and Union ministers Nitin Gadkari and Subhash Bhamre from Nagpur and Dhule seats respectively.
All Congress candidates, including former Union minister Sushilkumar Shinde, state president Ashok Chavan and Mumbai unit chief Milind Deora, lost the polls.
BJPs Sujay Vikhe Patil was leading over his NCP rival Sangram Jagtap in Ahmednagar.
The BJP nominee, son of Congress leader Radhakrishna Vikhe Patil, quit the Rahul Gandhi-led party to join the BJP ahead of the Lok Sabha polls.
In Maval, sitting Shiv Sena MP Shrirang Barne defeated his NCP rival Parth Pawar, the grand nephew of former Union minister Sharad Pawar.
In Mumbai-North, BJPs Gopal Shetty defeated Congress nominee Urmila Matondkar. In Raver, BJPs Raksha Khadse trounced her Congress rival Ulhas Patil.
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