Tyson pounced for the equalsier with 15 minutes to go before Whelan struck the winner 60 seconds later.
Sonny Carey’s free-kick has given the Linnets the lead in the first-half.
The win is Town's fifth in a row and cements their position in sixth in the National League.
Here are Liam Norcliffe’s player ratings from the match...
1. Grant Smith 7
Conceded his first goal in five matches when Carey's well-taken free-kick flew in from the edge of the area. Made a good stop to deny Carey from distance before that and did well to hold Kiwomya's strike late on. Photo: Dean Atkins
2. George Carline 9
Assisted both goals with crosses from the right and in general he was excellent. Almost scored with a header in the first-half. Photo: jason chadwick
3. Fraser Kerr 6
A few shaky moments but got better as the game went on. Gyasi caused him and Maguire some problems with his pace and trickey. Today was the first time he has experienced conceding a goal in a Town shirt. Photo: jason chadwick
4. Gavin Gunning 7
Made a welcome retun after his hamstring injury. His distribution was excellent. He bundled Jackson over on the edge of the box and Carey scored the free-kick which was his only big defensive lapse. He missed a sitter from six-yards out at 1-0 in the second-half. Overall he had a decent game. Photo: Michael South