On 21 minutes Bristol Rovers equalised with a freak goal. A clearance by Amankwaah struck Duffy's leg and the ball rebounded into the net to make it 1-1.
Phil Smith had to make a couple more good saves to keep Swindon in the game in the first half.
7 minutes of stoppage time were played in the first half after the injury when Swindon scored.
The second half looked like neither side would score before in the 81st minutes Cox scored his 30th of the season from 10 yards out.
The game was watched by 10,977, one of the highest crowds of the season, and the win moves Swindon up to 16th place on 52 points. As Carlisle could only draw 1-1 with Cheltenham this now makes Swindon safe from relegation for another season.