The striker sealed all three points from the spot after Wade Elliott was felled in the box as the Robins maintained their unbeaten start to the season.
Earlier Aaron Wilbraham’s 60th minute equaliser had cancelled out Zeli Ismail’s first-half goal.
On-loan Wolves winger Ismail put the hosts ahead in the 13th minute, racing onto a long ball and sliding past goalkeeper Frank Fielding.
But the Robins clawed their back into the game, with Luke Freeman hitting the post.
Steve Cotterill’s side were then given a let-off early in the second half when Liam Noble raced through on goal, only to shoot wide.
It was a gilt-edged chance and the Magpies were made to pay on the hour when Wilbraham finished off Mark Little’s cross.
And Emanuel-Thomas duly wrapped up the victory when he converted from the spot after a foul on Elliott late on.
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