Swindon went in front for the first team this season on 23 minutes when Sam Parkin headed in from inside the box.
Swindon's lead didn't hold out until half time as Smart scored for Milton Keynes with a close range effort on 42 minutes.
In the second half Swindon gave away their third penalty in three games, but this time Rhys Evans dived to his left and made a good save. This was Evans first ever penalty save that has counted, as last season he saved a penalty against Luton, but he had to be retaken, and they scored the second time around.
The penalty was the main turning point in the game when Howard playing up front in place of Rory Fallon scored with a good shot that just crept in.
Swindon were able to hold out for the win, but they didn't look like they were controlling the game. Milton Keynes were a poor side, and had it been a better team that Swindon would have lost the game.
Swindon's next game in next Saturday away to local rivals Bristol City in the Westcountry derby.