The 35-year-old Delhi batsman smashed 18 boundaries and a six in his 97-ball innings to help MCC overhaul the victory target of 225 in 51 overs on the fourth and final day.
Out of the national side for more than a year, Sehwag played a captain's knock as he added 105 runs with Samit Patel (48 not out)of Nottinghamshire for the fourth-wicket.
Sehwag was finally dismissed by Jamie Harrison in the 49th over of MCC's second innings.
The inexperienced Durham attack failed to tame Sehwag as he completed his half-century in 47 deliveries with the help of eight boundaries and then by lunch, he was only five runs short of the three-figure mark.
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Sehwag brought up his hundred shortly after the lunch break with a boundary off Harrison. He took 88 balls to reach his century.
Harrison, however, had the last laugh as he had the Indian caught by Paul Coughlin.
MCC finished the third day at 48 for two in 20 overs with Sehwag on nine and DJ Bell-Drummond on 15.