Sub Bond had only been on the pitch for seconds when he drilled home from Drey Wright's pass.
After the break, the U's slowly turned the screw and a goal was looking likely.
The first half of the game was goalless but both sides had opportunities to open their account for the season.
The late goal was coming for Joe Dunne's side, and the fantastic travelling support erupted as the scorer celebrated right in front of them.
It was no more than the U's deserved, with a patient game plan wearing down the Gills.
The U's opened the season with a great win at Gillingham, beating Martin Allen's side 1-0 thanks to Andy Bond's late strike.
Freddie Sears and Craig Eastmond both had shots wide and Sam Walker had to acrobatically tip a shot onto his own bar to prevent the Gills from scoring.
U’s boss Joe Dunne was without Sanchez Watt for the visit to the Gills but the signing from Arsenal was the only absentee.
It was the home side that started the game the strongest, with Charlie Lee crowded out in the second minute and Kedwell shooting wide from an angle.
Jabo Ibehre almost had the U’s first effort but he was inches away from a Brian Wilson free kick, given when Sears was fouled.
Craig Eastmond then got in the act as the U’s got a foothold in the game, shooting straight at Nelson after good work from Ibehre and Marcus Bean.
That came on thirteen minutes and five later, Ibehre flicked a near post effort just over from a low Sears cross into the danger area.
A minute later and Walker and the U’s were grateful for his height and flexibility. He stretched to tip a dipping strike from Kedwell onto the bar and away for a corner.
The game was opening up and Sears then cut inside from the left and whipped his effort just wide of the far post.
Walker then watched a header drop wide of is own far post and an Adam Barrett shot fly into the side netting as the home side responded to the U’s spell of pressure.
But the U’s were continuing the ask questions and Ibehre might have regretted taking a touch instead of shooting first time when the ball dropped to him inside the box.
Before he could get a shot away after a poor touch, Nelson was off his line and smothering the ball at the U’s forward’s feet.
More good U’s build up play in the thirty ninth minute saw Eastmond and Bean combine before the former shot wide from just outside the penalty area.
Walker then had his easiest save of the afternoon so far, as he comfortably gathered a free kick by Joe Martin.
As the first half went into added time, Wilson got forward from right back and his left foot shot was awkwardly palmed away by Nelson.
That was the final chance of the half and the U’s were more than holding their own against their Kent counterparts.
The second half began as the first had, with the Gills having the early pressure.
Wilson had to be alert as a through ball found McDonald and the U’s skipper’s last ditch tackle was needed as the Gills striker shaped to shoot.
It didn’t take the U’s long to get back on the ball though and Sears was the first U’s player to test the Gills’ defence.
Ryan Dickson got forward well from left back and found Sears, who turned inside and shot over from outside the box.
Dickson then produced a great cross for the advancing Bean, whose volley was well saved by Nelson.
While both sides were working hard in the middle third of the pitch, neither was testing the opposition keeper as the clock game reached its three quarter mark.
On seventy minutes, sub Weston had the chance to test Walker but he ballooned his shot over from another long throw into the box.
A minute later, Walker was thoroughly tested and came through with flying colours as a double save denied the Gills.
First he palmed away a shot from distance and with Weston looking to sidefoot home the rebound, the Chelsea loanee recovered to keep the scores level.
On seventy three minutes, Dunne made his first change of the afternoon, bringing on Alex Gilbey for the hard working Marcus Bean.
He was straight into the action, heading goalwards but being denied by Nelson in the home goal.
Just before Gilbey’s effort, Nelson had to save as Ibehre chested down a cross, turned neatly before shooting low to Nelson’s near post.
The second change for the U’s came on seventy seven minutes, as Drey Wright replaced Freddie Sears.
A rehearsed free kick didn’t quite come off for the U’s two minutes later, as David Wright’s effort flew well over from a pulled back Dickson set piece.
As the game went into the last ten, Linganzi shot straight at Walker, who was looking extremely comfortable in front of the U’s defence.
Gilbey repeated his feat of heading at Nelson with seven minutes to go, but the U’s youngster might feel that he could have gone either side of the Gills’ keeper.
A goal had been coming for Dunne's men and it was no more than the U's deserved for a great afternoon's work on the first day of the season.
And Bond put the U's ahead with his first touch, drilling home from fifteen yards out from a Drey Wright pass.
A Gills corner then led to Martin drilling a long distance shot just over the U’s bar, before Andy Bond replaced Eastmond in the midfield.