Merai was batting on unbeaten 121 off 220 balls laced with 19 boundaries and had also put on a solid 101 runs with Rakesh Dhurv (42 not out) when stumps were drawn.
Starting the third day on 216 for five, Gujarat added another 57 runs and took the score to 373 for six when the umpires stopped the play due bad light.
In the morning session, the visitors lost overnight batsman Akshar Patel after he put on a crucial 87-run stand for sixth wicket with the centurion Merai.
It was left-arm spinner KP Apanna who dealt a blow to Gujarat as he cleaned up Akshar for 39 off 69 balls with seven boundaries to his credit.
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The left-handed batsman Dhurv played a crucial unbeaten knock, which helped Gujarat take the first innings lead.
Brief scores:
Karnataka 1st innings: 306 all out
Gujarat 1st innings: 373 for six in 120 overs (Bhargav Merai batting 121, Rakesh Dhurv batting 42; Abhimanyu Mithun 2/82).