With Ely turning up late, the kick-off was delayed by 35 minutes meaning that most of the second half was played in dusk as well as the cold and driving rain.
Gav Taylor's penalty and Matt Fulcher's tap-in looked to have given Hundon victory but two late strikes left manager Brian Pilgrim feeling down in the dumps.
"I was gutted but at the end of the day you have to weigh it up on the whole season and we haven't been good enough to win the league," said Pilgrim.
"That summed us up last night. We were 2-0 up with seven minutes left and then just lost our heads."
Wayne Smith miscued in front of goal when he looked certain to score from three yards but it didn't seem to matter when Michael Chow was controversially penalised for a foul on Andy Palazon and Gav Taylor smashed home the penalty off the underside of the crossbar.
The home side pressed forward and created a number of chances, the best when Roger Dourado headed the ball against the bar.
Hundon inevitably doubled their lead when Matt Fulcher (right) was played through and the young striker exchanged passes with Smith around the visiting goalkeeper before tapping in.
The second half was a non-event for the first half-an-hour of it and the match looked to be petering out to a Hundon victory until Lee Clerkin was knocked out cold by a late challenge and Hundon were forced to play the final ten minutes with ten men.
In those final minutes James Arter squeezed a shot in past Matt Morrison and then Danny Mitchell saw his effort deflected past the helpless Hundon goalkeeper.
But after those two late strikes went in manager Pilgrim was philosophical about his side's achievements and believed Waterbeach deserve to go on to become the champions.
He said: "Waterbeach have such a strong team that have done it all before, it's half the old Fulbourn team that played in the Ridgeons League.
"Hundon are learning, it's our first season in there but I keep thinking 'did I mistake?'
"I keep winding it over in my head but at the end of the day we, I and the team weren't good enough.
"If we had started mediocre and then the last ten games played really well and won most of them to finish third people would have gone, 'bloody hell, Hundon have done well'.
"But because we've been up there so long and slid away at the end it does take the gloss off it."
Hundon lost 3-0 at Great Shelford on Saturday to set up Tuesday's make or break game.