Resuming on 304 for four in their second innings with Denly unbeaten on 119, the MCC harboured hopes of holding out for an unlikely draw on the fourth and final day despite following on after being dismissed for a paltry 130 first time around.
Rikki Clarke was the most successful Warwickshire bowler in the second innings as he finished with a total of four for 33 off his 12 overs.
Peter Trego continued where he had left off by adding 30 more runs to his overnight total of 57 before he was caught by Varun Chopra off the bowling of Oliver Hannon-Dalby for 87.
That wicket reduced MCC to 350 for five and when Ned Eckersley departed having added just one more run to that total their hopes of holding out for the draw began to look bleak.
After James Middlebrook succumbed to the bowling of Clarke for 17, Denly's heroic effort finally came to a close when he was also bowled by Clarke after an innings of 243 balls including 17 fours.
Warwickshire's victory was complete when Simon Kerrigan was the last MCC wicket to fall on 20 to the bowling of Chris Wright, who finished with figures of three for 75 off 19.5 overs.
Warwickshire had seized control of the game by declaring on a first innings total of 561 for six, an innings from which Denly was forced to retire on day two suffering from a migraine.
And the MCC were always up against it after being skittled for just 130 in their first innings response, with Wright claiming five for 35 and Hannon-Dalby three for 30.
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