However, the win came at a price with three other injuries adding to Vince's woes with the first league game against Bamber Bridge a little over a week away.
Vince already had Adam Morning, Ryan Sugden and Tom Harban in the treatment room and now has Kris King, Neil Ross and Junior Brown queuing up to join them.
Highly-rated Stott, who showed his pace in the 1-0 defeat at Guiseley last Thursday was given a run out from the start and he went closest to opening the scoring with a shot from distance.
Halifax continued to create chances and Ben Jones, who had come on for Ross, almost made an impact with a shot that came back off the crossbar.
The same player suffered a similar fate after the break as Halifax overcame their hosts' rough-house tactics to pose plenty of threats in front of goal.
Their positive approach finally paid dividends and it was Payne who found the net first, rising highest to nod home Dorryll Proffitt's cross.
That was the breakthrough Halifax needed and they went on to extend their lead minutes later, this time Stott being in the right place to head home Junior Brown's cross from close range.
Halifax continued to press but found no further reward leaving Vince to pay tribute to his side for their conduct in the face of some heavy challenges.
FC Halifax Town: Mawson, Hinsley, King, Payne, Adams, Smith, Clegg, Walker, Stott, Ross, Brown, Senior, Rothery, Jones, Proffitt, Jemson.