The Tudors began on the front foot and created the early opportunities.
But midway through the half came the first controversy of the evening when Jamal Lowe burst forward and looks to be tripped from behind, but instead the referee booked the Hemel man for diving.
Tudors` manager Dean Brennan was subsequently sent to the stands for his continued protests about Lowe's booking.
And he saw his side suffer a sucker punch right at the end of the half as Ross Stearn slotted home on the rebound after a fine save from Jamie Butler from the initial effort.
Sutton almost doubled their lead immediately after the break through Kevin Amankwaah, whose effort struck the bar and bounced clear. Then Sutton manager Paul Doswell joined his counterpart in the stands for something he said to the linesman.
The hosts made it 2-0 when substitute Dan Wishart cut in from the left and slotted the ball past Butler into the bottom corner.
Hemel did manage to pull one back in the 3rd minute of stoppage time through Ben Herd, but it was too little too late to prevent their FA Cup exit.