The former Southend United forward scored twice as Port Vale were beaten 4-0 in the third round of the FA Cup.
They were his first goals on home territory after he grabbed the winner at Newcastle United back in August.
The £500,000 summer buy notched 17 times for Southend.
However Wagner, whose side are back on Championship duty at Sheffield Wednesday on Saturday, played both against Port Vale.
He had done the same in a training-ground friendly at Liverpool in September - both Payne and Palmer scored as Town won 2-1 at Melwood.
“That game was in my mind when I made my plans for Port Vale,” explained Wagner. “They both did well in that game, and it was the same on Saturday.
“To go without a natural No9 is a bit different to what we have done in past.”
Wagner, whose side are fourth, added: “We know what a good player Jack is.
“We have spoken a lot about his end product, how he has to make sure he hits the target.
“He not only hit the target against Port Vale, but the net too.
“This is one of the areas he has to work on.
“Jack has great skills, and can be a very dangerous player in final third.”