Amankwaah was left unmarked at the far post to volley in the winner deep into injury time, but Clarets boss Mark Hawkes was left seething after Tom Lovelock appeared to have been fouled by Craig Dundass in the build-up.
The result leaves Chelmsford 12th in the league following their third straight defeat, with the side only picking up one win in their last nine outings.
With that recent run of form putting the Clarets out of contention for the play-off places, there was little riding on the result this afternoon with Sutton clear of any immediate danger of dropping into the relegation zone.
And with both sides finding goals hard to come by in recent weeks it was little surprise that the first half produced only a handful of opportunities in front of goal.
Tom Lovelock – who was returning to Sutton for the first time since his move to Chelmsford earlier this season – would have been pleased to see all of his former side’s efforts in the first period coming from distance as the hosts failed to test their former custodian.
City were finding goal chances hard to fashion themselves but were given a helping hand by Sutton. Kevin Amankwaah played the ball back to Howe who handled, leaving the referee to award an indirect free kick for the back-pass, but Rohdell Gordon failed to hit the target as his shot curled wide.
With the half time approaching, top-scorer Michael Cheek wriggled his way clear only to see his low strike saved by the legs of Aaron Howe, and Chelmsford felt they should have had a penalty late on when Mark Haines went down in the box, only for the referee to award a free kick to the home side.
The second period began in the same vain as the first, with chances few and far between. But midway through the half the game sparked into life and Lovelock showed what his old side were missing with a number of top-drawer saves.
Amankwaah was first to be denied by the City ‘keeper when his free header was brilliantly tipped over the bar by Lovelock. Minutes later Lovelock again denied his former side when he got down low at his near post to prevent Dan Wishart’s free kick from creeping in.
Up the other end and Cheek went closest to opening the scoring for City when he went up for a high, bouncing ball with Howe only for the City striker to beat the goalkeeper but fail to direct his header on target with the goal gaping.
Cheek was then left perplexed when he appeared to have been blatantly chopped down in the area by James Collins, but the referee was unmoved despite Cheek's and his manager’s protestations.
Lovelock was then called upon again having to punch away a free kick from Damian Scannell before coming out quickly to stop Bedsente Gomis after the ball had fallen kindly to him in the area, smothering the chance.
But with the game looking like it was going to end in a stalemate the hosts nicked all three points in the fourth minute of stoppage time through their right back, Amankwaah.
A corner on the Sutton left was whipped towards the far post with Lovelock looking to claim. As he went up for the ball he was barged in the back by Dundass, allowing Amankwaah to loop the ball back into the unguarded net and steal the win for the home side.
1. Aaron Howe
2. Kevin Amankwaah
3. Dan Wishart
4. Micky Spillane
5. Kieron Forbes
6. James Collins
7. Damian Scannell
8. Glen Southam (C)
9. Craig Dundas
10. Dan Fitchett
11. Louie Theophanous
12. Ricky Wellard (On for Louie Theophanous 70’)
14. Dale Binns (On for Micky Spillane 70’)
15. Bedsente Gomis (On for Dan Fitchett 65’)
16. Callum Hart
17. Wayne Shaw
1. Tom Lovelock
2. Harry Hickford
3. Michael Toner
4. Leon Redwood
5. Mark Haines (C)
6. Marvin Ekpiteta
7. Harry Morgan
8. Joe Ward
9. Rohdell Gordon
10. Michael Cheek
11. Mason Spence
12. Sam Gregory
14. Evans Kouassi (On for Mason Spence 72’)
15. Lee Sawyer
16. Kevin Maher
17. Rob Girdlestone
Referee: Tim Wood
Assistants: Stuart Cheek & Dele Sotimirin
Sutton United: Kevin Amankwaah 90 + 4’
Chelmsford City: None
Sutton United: None
Chelmsford City: Rohdell Gordon (Foul – 81’), Michael Toner (Foul – 87’)
City Man of the Match: Tom Lovelock