Exeter were made to pay when the Millers were also awarded a penalty and Reuben Reid put his side level from the spot.
Exeter started brightly and Liam Sercombe had a fine volley from the edge of the box tipped over brilliantly by David Stockdale.
Rotherham began to enjoy most of the possession and Peter Holmes shot at Paul Jones following a mistake by City defender Dean Moxey.
Exeter began to look dangerous as the half wore on and Ryan Harley struck the ball just over the bar after swapping passes with Marcus Stewart.
Moxey struck a close-range strike past the post before Exeter finally took the lead four minutes before the break. Manny Panther picked out Watson with a low cross and the striker made no mistake with his shot.
After the break the Millers enjoyed plenty of possession and Dale Tonge forced Jones to save well with a fine strike from 20 yards.
Exeter should have gone further ahead just before the hour mark. Watson twisted and turned and was adjudged to have been fouled inside the box by Marc Joseph. Watson stepped up to take the spot-kick himself but his effort was superbly saved by the inspired Stockdale.
Rotherham were level in the 66th minute when Fred Murray fouled Barker and Reid struck the resulting penalty right footed past Jones.
Exeter almost grabbed victory in the closing stages when Basham's fine cross was met by Harley and his header was superbly kept out by Stockdale.
Both sides went in search for a winner but had to be content with a point apiece.