The Glasgow star and Hewett fell short of the doubles gold they craved and both lost their singles semi-finals in a traumatic 48 hours.
Reid’s 6-4 3-6 7-5 win over Hewett earned him a fourth Paralympic medal, completing a set of gold, silver and bronze, but did nothing to numb the pain.
“The last thing we wanted to do was come and play against each other on the same court,” said Reid.
“I’ve cried more this week than I have the rest of the past three or four years.
“It doesn’t feel like I’m a winner at the moment but once the emotions settle down, I’ll be proud of getting a medal.”
Neither player celebrated winning a point and team staff remained silent in a Centre Court atmosphere that resembled a morgue.
Hewett battled back from 5-2 down to 5-5 in the third set but Reid used his power to pull away and wrap up victory in two hours and 22 minutes.
It was a repeat of the Rio 2016 gold medal final in the worst possible circumstances.
Hewett said: “We both said how much hated that match.
“It was horrible. There wasn’t much we could say to each other at the net at the end, we understood where we were both at.”
It played out against the backdrop of Hewett’s ongoing battle to save his place in the sport after his hip impairment was ruled not serious enough for him to compete.
Hewett, 23, will be ineligible come the end of the year if he doesn’t win an appeal and this month’s US Open could be his last major tournament.
“This is what I’ve done since I was eight years old,” he said. “It’s my career, it’s my profession and I want to continue.”
The harsh judgement could leave Reid of a doubles partner with whom he has won Wimbledon and the French Open four times, dominating the discipline in recent years.
“It’s tough for everybody involved with Alfie,” said Reid.
“It’s more evident than ever this week - the emotions everyone’s feeling.
“It’s not something that ever happens in sport - sometimes in disability sport, but not somebody who’s been playing for so long. It’s a difficult thing.
“I’ve seen Alfie grow from junior to best player in the world. I’ve been part of that journey with him as a partner and a rival so hopefully it’s not the end of the story.”
Reid has played with Belgian Joachim Gerard among others in the past but finds it hard to imagine a future on the court without Hewett.
“I’ve played with other people before. If I have to do it, if it comes to that, obviously I’m a professional and I’ll go and do that,” said Reid.
“But it’s impossible to replace Alfie. There’s not another Alfie Hewett in the world to play doubles with.
“I doubt I’ll ever have a bond with anybody on a tennis court like I do with Alfie because we’ve put so much effort and time into working together in this partnership.”
The bronze medal adds to Reid’s haul of gold from Rio de Janeiro in 2016 when he took the singles title and runners-up silver with Hewett in the doubles.
Meanwhile, Scottish wheelchair racer Ben Rowlings will be hoping for third time lucky in Paris after a frustrating Paralympics in Tokyo.
Rowlings finished last in the final of the T34 100m earlier this week and produced the same result over two laps, as heavy rain made racing tough.
"It was a difficult one and I'm a bit frustrated," he said, after clocking 1:48.63, over nine seconds off his personal best.
"I thought I got myself in a really, really good position behind the two big contenders with about 500 metres to go. I just didn’t kick hard enough to go with them, it wasn’t there but it is what it is.
"I can’t be too down and negative. Five years ago in Rio I didn’t get that chance, so to be in that race was a big achievement but I would have liked to do a lot better."
Rowlings will now target next year's World Championship, back here in Japan in Kobe, while a Paris Games is just three years away for the 25-year old.
And he knows the standard, Tunisia's Walid Ktila taking gold in 1:45.50 - not a huge distance away from Rowlings.
"I've got something to work on over the winter, it’s a step in the right direction," he added.
"I'm not a fully funded athlete yet so I have to juggle work and training but that's got to be my ambition.
"I’ll make sure I’m in as good as shape, if not better shape coming into next year."
The Games come to an end on Sunday morning with the closing ceremony handing over to the 2024 hosts Paris.
The theme of the handover following a successful staging of the 16th Games, has been announced as “Harmonious Cacophony”. Organisers said: “A world inspired by the Paralympics, one where differences shine. In this world, diverse bodies, unique technologies, and different materials all come together as a harmonious and colourful whole, not as a single blended colour, but each one shining as they are.
“What seems at first like the start of a cacophony is actually the birth of a new harmony. Because differences do not create conflict, but give rise to a new future.”