BJP candidates are leading with comfortable margins in three other assembly seats.
Out of the 28 seats which were up for grabs in bypolls, the ruling BJP has won 16 so far and is leading in three others (Sanver, Jaura and Mehgaon), according to the Election Commission (EC) data.
The opposition Congress has managed to secure victory in seven seats and is leading in two others (Dimani and Gwalior-East) with comfortable margins, the data showed.
In the 230-member House, the BJP tally has increased to 123 (well above simple majority mark of 116) with the addition of these 16 seats, providing stability to the Shivraj Singh Chouhan government.
Before the bypolls, the BJP's tally in the House stood at 107.
In Sanver, Scindia loyalist Tulsi Silawat is leading by a margin of47,947 votes against Congress candidate Prem Chand Guddu.
BJP minister OPS Bhadoria is leading in Mehgaon by a margin of 12,021 votes, while his party colleague Subedar Singh Rajoudha is ahead by 13,478 votes in Joura.
BJP minister Girraj Dandotiya is trailing in Dimani by a margin of 26,178 votes against Congress candidate Ravindra Singh Tomar.
The saffron partys nominee, Munna Lal Goyal, is trailing by a margin of 7604 votes against Congress candidate Dr Satish Sikarwar in Gwalior-East.
However, in a setback to the BJP, its woman minister Imarti Devi lost bypoll from the Dabra assembly seat, an election official said.
Congress candidate Suresh Raje defeated Imarti Devi, considered a loyalist of Scindia, by a margin of 7,633 votes, the official said.
State Congress president Kamal Nath's "item" jibe at Imarti Devi during campaigning had generated a controversy and invited criticism. The former chief minister later expressed regret over the comment.
Though the Congress left no stone unturned in portraying Scindia as a traitor because of his rebellion against the Kamal Nath government that paved the way for the BJP's return to power, the campaign plank failed to find much traction among voters.
Scindia has repeatedly said his decision to quit the Congress was driven by "failure" of the erstwhile Nath government to fulfil promises made to people, especially farmers.
The BJP's victory in these bypolls will certainly strengthen Scindias position in the BJP at the Centre, a political analyst said.
However, the BJP suffered some loss in the Gwalior- Chambal region where two of its ministers, Adal Singh Kansana (Sumaoli) and Imarti Devi, faced defeat.
The BJP narrowly won Bhander, where its nominee Raksha Santram Saronia defeated popular Dalit leader Phool Singh Baraiya by a margin of 161 votes.
Besides, a Scindia's supporter also lost in Karera in Shivpuri district.
There are a total of 34 seats in the Gwalior-Chambal region of which the Congress had won 26 in the 2018 assembly polls.
"Bypolls were held on 16 seats in this region and among them Scindias supporters are set to win nine seats which were earlier with the Congress. That is more than 60-70 per cent (of seats where bypolls were held in the region), state BJP spokesman Pankaj Chaturvedi said.
Earlier, the Congress had won more than 80 per cent of these seats because of the Scindia factor, he said.
Scindias supporters won decisively in Bamori, Mungaoli and Ashok Nagar, assembly segments falling under the Guna parliamentary constituency, once represented by him.
Among the six ministers who resigned from the Congress along with Scindia, only Imarti Devi lost in the by-poll.
Others like Silawat, Mahendra Singh Sisodia, Govind Singh Rajput, Dr Prabhuram Choudhary and Pradyumna Singh Tomar won decisively from their respective constituencies.
Choudhary won with a huge margin of 63,809 votes - the highest so far - from the Sanchi (SC) seat.
Elated over the BJPs performance, Chief Minister Shivraj Singh Chouhan said the outcome proves voters supported the decision taken by Congress MLAs to pull down the previous Kamal Nath dispensation.
"It has been proved today that public has supported the decision taken by our MLA colleagues under the leadership of Scindia (BJPs Rajya Sabha member Jyotiraditya Scindia) to pull down the (Nath) government," Chouhan told party workers.
He said the BJP has secured 11 per cent more votes than the Congress and termed it as an "incredible" achievement.
We won seats with huge margins and lost few with thin margins. We humbly accept the victory, the CM said.
On the other hand, Nath accepted defeat and said the party made efforts to reach out to people.
"We accept the mandate. We made every effort to reach out to voters. I also thank all voters who participated in the by-elections.
"I hope that the BJP government will take care of the interest of farmers, provide employment to the youth, maintain the respect and safety of women," Nath said in a tweet.
In March, 22 Congress MLAs, mostly loyalists of Scindia, had resigned from the party and the Madhya Pradesh Assembly.
This led to the collapse of the Nath government and cleared the way for the BJP to again come to power.
Scindia and his loyalists joined the BJP, with many of them becoming ministers in the Chouhan government.
Voting for by-elections on 28 constituencies was held on November 3 and counting of ballots was taken up on Tuesday.