Rishi Dhawan struck an unbeaten 117 while Robin Bisht scored 84 as Himachal Pradesh put on board 295 for five after being invited to bat.
Dhawan hit 13 boundaries in his 88-ball fiery knock.
HP bowled out Madhya Pradesh for 254 and finished on top of the table with four wins from five matches.
The other team to qualify for the knockout stage was Uttar Pradesh, who finished second in Group. UP also had four wins to show but Himachal's NRR was better.
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Brief Scores:
Himachal Pradesh: 295 for 5 in 50 overs. (R Dhawan 117 not out, R Bisht 84; C Sakure 1/37).
Madhya Pradesh: 254 all out in 46.1 overs.(V Iyer 57, P Sahani 42; P Jaiswal 6/40).