The response from Kansas was impressive, and they were back on level terms just before the half hour mark when Dom Dwyer brought down a lobbed pass from Krisztian Nemeth before drilling the ball past Brad Knighton.
Kansas took the lead 10 minutes later when the influential Nemeth lost his marker to head in from Benny Feilhaber's inviting free kick.
New England were stunned by the fightback, and they were dealt a further blow before the interval when Jose Goncalves foolishly brought down Dwyer inside the box.
Feilhaber stepped up from 12 yards to send the penalty past Knighton as the home side reached the break in complete control.
Kansas looked to have wrapped up the win when they made it 4-1 just 20 seconds into the second half as Nemeth linked up with Jacob Peterson before finishing calmly for his second of the match.
However, the deficit was reduced after the hour mark when Charlie Davies created space on the wing before pulling the ball back to Scott Caldwell, who kept his composure from 10 yards to slot past Tim Melia.
Davies almost made an impact once again when a corner eventually dropped to him in the box, but he could only slice an effort over the crossbar.
New England continued to push for a way back into the match, with substitute Chris Tierney's free kick being kept out by Melia as Kansas clinched all three points.