The alliance won 41 of the 48 seats leaving the Congress-NCP combine with just 5 seats.
The Bharatiya Janata Party-Shiv Sena combine won 41 of the 48 Lok Sabha seats in Maharashtra, while the Congress won one and Nationalist Congress Party 4 seats.
Two Union ministers and two former chief ministers tasted defeat in the election, which saw the Sharad Pawar-led NCP managing to retain its tally, while the Congress bagged just one seat, down from two it won in 2014.
The BJP-Sena ruling alliance had secured 42 seats in 2014 elections.
The All India Majlis-e-Ittehadul Muslimeen got its first MP from the state as its nominee Imtiaz Jaleel won from Aurangabad, defeating the Sena nominee Chandrakant Khaire.
Congress candidates, including former Union minister Sushilkumar Shinde, state president Ashok Chavan and Mumbai unit chief Milind Deora, lost the polls.
Sujay Vikhe Patil defeated 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.
The 23 Lok Sabha seats BJP won are Nandurbar, Dhule, Jalgaon, Raver, Akola, Wardha, Nagpur, Bhandara-Gondiya, Gadchiroli-Chimur (ST), Nanded, Jalna, Dindori (ST), Bhiwandi, Mumbai North, Mumbai North East, Mumbai North-Central, Pune, Ahmednagar, Beed, Latur (SC), Solapur (SC), Madha and Sangli.
Maharashtra minister Girish Bapat of BJP comfortably won from Pune Lok Sabha seat against Congress candidate Mohan Joshi.
The Shiv Sena won Buldhana, Ramtek (SC), Yavatmal-Washim, Hingoli, Parbhani, Nashik, Palghar, Kalyan, Thane, Mumbai North West, Mumbai South Central, Mumbai South, Maval, Shirdi (SC), Osmanabad, Ratnagiri-Sindhudurg, Kolhapur and Hatkanangale seats.
The Sena made inroads in Kolhapur, snatching it from NCP but its sitting MPs from Amravati, Aurangabad and Shirur were defeated. The Sena's lone Union minister Anant Geete lost to NCP's Sunil Tatkare in Raigad Lok Sabha seat.
NCP won four seats this time as well, but lost Kolhapur and Madha and gained Shirur and Raigad seats.
The BJP and Shiv Sena contested 25 and 23 seats respectively. Congress fielded its candidates in 25 seats while NCP contested 19 seats. The Congress-NCP had shared the remaining four seats with their allies.
Union minister Nitin Gadkari comfortably won the Nagpur Lok Sabha seat by a margin of 2,16,009 votes.
WATCH: Gadkari retains Nagpur seat with a margin of over 2 lakh votes
A former BJP president, Gadkari retained the seat by defeating his nearest Congress rival Nana Patole. Gadkari polled 6,60,221 votes, while Patole got 4,44,212 votes at the end of counting spread over 20 rounds.
In 2014, Gadkari had won the Nagpur constituency, which this time voted in the first phase on April 11, by a margin of 2,84,828 votes.
Union minister Subhash Bhamre won from Dhule. The BJP candidate polled 6,13,533 votes, while his Congress rival Kunal Patil got 3,84,290 votes.
The BJP suffered a setback in Chandrapur, where Union minister Hansraj Ahir lost to Suresh alias Balu Dhanorkar of the Congress by a margin of 44,763 votes.
This is the only Lok Sabha seat won by the Congress in Maharashtra, which sends 48 members to the Lok Sabha.
Dhanorkar, a sitting Shiv Sena MLA before joining the Congress ahead of elections, secured 5,59,507 votes, while Ahir got 5,14,744 votes.
In 2014, Ahir had won from Chandrapur by a margin of 2,36,269 votes.
In Raigad, Shiv Sena leader and Union minister Anant Geete lost to NCP's Sunil Tatkare. While Tatkare got 4,86,968 votes, Geete polled 4,55,530 votes.
Navnit Rana, who contested as an independent from Amravati won the election against Sena veteran Anandrao Adsul.