Mr Rawat lost the Kichcha seat by less than 100 votes to incumbent Rajesh Shukla of the BJP and the Haridwar seat by a margin of around 9,000 votes to his BJP rival Yatishwaranand.
Five years ago, the BJP had lost Uttarakhand to the Congress by a whisker. The party had won 31 seats, the Congress 32 - both short of the 36 needed to form government. The Congress later formed the government with the help of Mayawati's Bahujan Samaj Party or BSP and others. The BSP had failed to win any seats in the hill state this year.
Last year, Mr Rawat survived a trust vote following a rebellion in his party. Several Congress leaders changed camp since, pushing the BJP into a tight corner to choose the right candidates for the election. The party also had to quell protests from its long-time state leaders when the new imports were fielded.
On Thursday, three exit polls predicted that the BJP will get a landslide victory a fourth said the BJP and the Congress will have a tie. The aggregate -- the poll of exit polls - showed that the BJP will decisively winning the hill state with 42 seats. The Congress, the aggregate showed, will win 24 seats.
The BJP also is headed for a landslide victory in neighbouring Uttar Pradesh - at 3.15 pm, the party was leading in 316 of the state's 403 seats.
Speaking to NDTV, BJP national secretary TS Rawat said, "UP and Uttarakhand are in themselves like elder brother and younger brother. Like Atal-ji's (Atal Bihari Vajpayee's) vision gave us Uttarakhand in 2000, under Modi-ji we have today won a decisive and historic mandate in Uttarakhand as well. Modi-ji's management and Amit Shah's management on the ground are visible today."
The Congress, for its part, said it would wait for the ECs final numbers to gauge the scale of their loss, although state congress chief Kishore Upadhyay conceded, "Whatever the mandate of the people is we have always accepted that and accept it today as well. I have come to see the Chief Minister before he proceeds to the Governor's house".