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Gujarat were 104 for the loss of one wicket when the stumps were drawn at the Sardar Patel Stadium, Motera.
Opener Samit Gohel (43) and Bhargav Merai (28) were at the crease.
Left-arm spinner Gajendra Singh got the wicket of young opener Smit Patel who scored just 27 runs.
Earlier, Rajasthan finised their first innings at a reasonable total, thanks to Kanitkar's 100 that included 13 boundaries.
For Gujarat, left-arm spinner Rakesh Dhruv finished with an impressive figures of six for 65 in 45 overs, including 21 maidens.
Gujarat are trailing the visitors by 190 runs with nine wickets remaining in their first innings.
Rajasthan: 1st innings: 294 all out 127 overs (Hrishikesh Kanitkar 100 not out, Sourabh Chouhan 42; Rakesh Dhurv 6/65)Gujarat 1st innings: 104/1 in 54 overs ( Samit Gohel 43 not out, Bhargav Merai 28 not out; Gajendra Singh 1/18).