The AIADMK candidates won the Vikravandi and Nanguneri Assembly seats while Congress party won the Kamaraj Nagar seat in Puducherry.
AIADMK's R. Muthamilselvan won from Vikravandi, polling 113,428 votes while his DMK rival N. Pugazhenthi had polled 68,646 votes.
In Nanguneri, AIADMK candidate V.Narayanan polled 94,802 votes while his Congress rival Ruby R. Manohar had polled 61,991 votes.
The bypoll in Vikravandi was necessitated following the death of DMK legislator K. Rathamani in June, while the Nanguneri seat fell vacant after Congress legislator H. Vasantha Kumar got elected to the Lok Sabha and resigned.
A total of 35 candidates were in the fray in the two seats.
Speaking to reporters, Chief Minister K.Palaniswami said the alliance led by the DMK won the Lok Sabha elections because of their "false promises". "But now the people have realised that and have voted for the AIADMK."
This victory is a forerunner for the next Assembly elections for the ruling combine, he added.
The poll reversal is a setback for the DMK and Congress as they lost the seats held by them. This defeat comes close on the heels of the DMK-led alliance winning 38 Lok Sabha seats out of 39 in Tamil Nadu in the general elections held in April.
In Puducherry, the Congress retained the Kamaraj Nagar Assembly seat.
Congress' A. John Kumar won the polls with 14,782 votes, defeating his nearest rival and AINRC party nominee S. Bhuvaneswarane, who managed 7,611 votes.
The seat fell vacant after Congress legislator V. Vaithilingam was elected to the Lok Sabha in April this year.
( With inputs from IANS )