The visitors required 155 runs to avoid an innings defeat with the hosts declaring their innings at 469 for 7.
Karnataka added 42 runs to their overnight 427 for before losing centurion Krishnappa Gowtham in the first hour of the day.
The all-rounder, who was batting on 147, added only two more runs before he was caught and bowled by Arup Das.
He cracked ten boundaries and six sixes in his 149, which came off 170 deliveries.
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For Assam, Arup Das toiled for 41 overs for his four wickets while Swarupam Purkayasta scalped three wickets, though he was a bit expensive
When Assam batted, Krishnappa Gowtham did bulk of the damage.He has picked up seven wickets altogether in the match.
The forecast for tomorrow is quite grim with rains forecast.
For Assam, skipper Gokul Sharma cracked his second 50 of the match. The visiting captain is batting on 62, which came off 111 balls with six exquisite boundaries.
Brief scores: Assam 145 in 59.1 overs and 169 for 6 vs Karnataka 469 for 7 in 115 overs (K Gowtham 149, Ravikumar Samarth 123).