Former Port Vale, Swindon and Leeds striker Paynter's brace completed a quick-fire comeback for Doncaster, who stay two points ahead at top of the table.
Max Clayton had fired Crewe ahead, but Paynter came off the bench and netted twice in four minutes to ensure Rovers stayed in pole position.
Oliver Turton blew a late chance to earn the Alex a draw they arguably deserved as Crewe suffered their second defeat in a week since lifting the Johnstone's Paint Trophy.
Davis said: "Billy Paynter made a big impact. He is a goalscorer and has played at a higher level.
"That is what teams have a big budget for so they can afford players like that who can come and make an impact for you off the bench.
"Oliver Turton should have scored for us and I think a draw would have been a fair result.
"We have been encouraging him to get into those positions for us and situations like that have got to go in the back of the net.
"I was pleased with how the players responded after the midweek defeat, there was some decent performances and we learned a lot about some of the players who haven't played so much before.
"They were a big, strong forceful team and that is what seems to get you to the top of this league. I wouldn't want to play that way, we are always going to try and get it down and play."
Alex broke the deadlock in the 54th minute.