Dixon was taken off after just half an hour after badly pulling a hamstring and could face a stint on the sidelines for up to a month and he was joined in the treatment room by ex-Welsh international Barnard, who twisted his knee under a poor challenge from Daggers' midfielder Bai-Mas Lette Jallow.
He too could now miss out on this Saturday's trip to Kidderminster Harriers.
With the Shots already down to bare bones due to a distinct lack of strength in depth in both defence and attack, the boss admits it could cause him a problem.
“We're hoping Barney's just got a dead leg, the doctor checked it out and said there's not cartilage or ligament damage so we're hoping rest will sort it out.
“Dixon's another problem he could be out up to four weeks, and with the size of our current squad I don't quite know what I'm going to do.
“Our home form's been good but we've got to turn that round at Kidderminster on Saturday and we've got to do that without Barnard and Dixon who are important players,” said Brown.
Still, the loss of Dixon didn't cause the Shots too much trouble as they eased past a lacklustre Daggers side with three of the highest quality goals seen at the Rec this season.
It was Barnard who kicked off proceedings with a shot from distance, Ryan Williams added the second before a superb athletic over-head goal from man of the match Gary Holloway sealed the points.
“Gary's effort could have gone anywhere, I saw the whole East Bank duck! He deserved the man of the match, he had a smashing game and worked very hard and for once I can say we defended well.
“Two was never going to be enough, it's not a 1-0 side, more like 4-3. Our strengths are attacking and getting at people and scoring goals. We missed a lot of chances but overall I'm delighted with the win over what I consider a very good attacking side,” added Brown.
The boss brought Leroy Griffiths back to the starting line-up after he was dropped for the Accrington game after failing to turn up to training but not for the first time this season, Brown was only able to name four substitutes to occupy a youthful bench to say the least.
This was an impressive performance, albeit against an unusually quiet Dagenham side which allowed the Shots to run riot with crisp passing and some slick football.
The Shots started brightly, winning a corner in the first minute, only for Ryan Williams to see his shot was blocked.
Jonny Dixon then headed just wide of the post from Williams' curling delivery and then saw an effort ruled out for offside, latching onto a rebound from Daggers keeper Tony Roberts.
The Shots were really dominating by this point and should have had a penalty when Danny Foster denied Holloway with the net gaping after Roberts had failed to collect from Dixon.
On 20 minutes the Shots finally got the goal they deserved.
A corner kick was half-cleared to Barnard, who let fly with a rasping drive from 25 yards which bounced in off the far post to the delight of the Rec.
The joy though was short-lived as Dixon gave Brown his first headache of the afternoon, limping off on the half-hour mark to be replaced by youngster Kirk Hudson.
The Daggers responded with Sam Saunders bringing out a save from Nikki Bull from another dangerous free-kick, while the pacy Craig-Mackail-Smith left Greg Heald in his wake, only to be thwarted by the covering Lewis Hamilton but with half-time looming and Brown preparing his interval speech, the Shots doubled their lead.
Williams burst down the wing to chase a good ball from Steve Watson and after playing a neat one-two with Leroy Griffiths, slotted coolly past Roberts.
The second half saw much the same pattern of play after early Dagenham promise — Hudson unleashing a fierce shot which Roberts spilled for a corner, and then Heald nodded over from the resulting corner.
Minutes later the lively Hudson fired just wide of the post, this after Leroy Griffiths got the better of Anwar Uddin to square to his strike partner.
At the other end, Bull pounced on a cross-cum-shot from Mackail-Smith, but moments later the Daggers got themselves back in the game.
Chris Moore shrugged off Hamilton all too easily in the box, allowing him to cross to an unmarked Mackail-Smith at the far post, gifting him a simple tap-in past Bull.
Aldershot's misery was compounded moments later by the sight of Barnard writhing in pain from Lette Jallow's challenge.
The booking did little to stop the tenacious midfielder in his tracks and shortly afterwards, was lucky to stay on the pitch with a poor challenge on Holloway. Referee Simon Beck, well-known to Shots fans this season after sending off two of their players, failed to even book the player.
However, the Shots soon added their killer third to seal the win — and what a goal it was!
Williams floated over a corner and Tobi Jinadu nodded down for Holloway to fire a sublime overhead scissor-kick past Roberts, much to his obvious delight.
The Shots went close to adding a fourth late on, Roberts denying Leroy Griffiths from Hudson's through-ball, while Bull, at the other end, made an excellent save at the post from Scott Griffiths' close range effort to keep the Daggers at bay.
The result lifts the Shots above their rivals into 13th spot, and gets their impressive home record back on track.
“The Rec is a fantastic place to play football, I'm always complimentary to the crowd, they're fantastic, they're supportive, and for their sake it's lovely to win for them,” added Brown.
With just ten games left of the season, the boss is already planning ahead for next season, and hopes to have Crawley centre half, and former Woking player, Ian Simpemba on board by the end of the week.
Despite what has been a rather anti-climatic season after the highs of the play-offs for two seasons running, Brown still believes there is everything to play for.
He added: “When you're playing at the Rec and you're manager of Aldershot, every home result means everything, that's what my supporters wait all week for, to watch the Shots win.”
“We aim to keep doing that and the boys are every focussed on picking up as many points between now and the end of the season."
With thanks to the Aldershot News.