The 26-year-old, who was an unused member of England’s Test squad which toured South Africa over the winter, made 105 in the traditional curtain raiser against a strong attack featuring England internationals Graham Onions, James Tredwell, Rikki Clarke and Samit Patel.
The 21-year-old Will Rhodes also chipped in with 95, but MCC arguably finished the day on top as the last five wickets fell for 62 runs.
Yorkshire start their quest for a third consecutive Specsavers County Championship title next month, but found themselves 88 for five shortly after lunch as Tredwell picked up three wickets.
Nottinghamshire’s Jake Ball made the initial breakthrough when he trapped Alex Lees lbw for a duck in the second over, and Clarke swiftly accounted for Adam Lyth.
Kent’s Tredwell then had Andrew Gale and Tim Bresnan caught by wicketkeeper Ben Foakes either side of bowling Jack Leaning.
Ballance and Rhodes then repaired much of the early damage, sharing a stand of 125 for the sixth wicket.
Patel eventually trapped Ballance lbw and the end of the left-hander’s innings sparked another collapse.
Andrew Hodd was bowled by Ball, and Onions dismissed Steven Patterson and Jack Brooks with successive deliveries before Rhodes was last man out – caught behind off Clarke five short of his ton.
Tredwell’s 3-53 was the pick of the bowling figures, with Ball, Clarke and Onions picking up two wickets each.
Nightwatchman James Harris, thrust in to open, then saw out a solitary over from Brooks before stumps as MCC began their reply.