The two long-term absentees completed their first 90 minutes this season for the reserves against Stoke City after lengthy rehabilitation, while striker Ramon Nunez pressed his claims for a first-team debut with Leeds' goal in a 2-1 defeat.
Simon Grayson said: "Ben and Billy both played 90 minutes which was pleasing and the likes of Leigh Bromby, Alex Bruce and Aidy White all got some important time on the pitch.
"The injuries are taking shape again now with a few more coming back into contention."
Left-back Parker has been out of action for over a season due a succession of injuries and striker Paynter has yet to make his first appearance for Leeds since arriving in the summer from Swindon due to a shin injury sustained in a pre-season friendly.
Source: PA