Rutherford, 26, suffered a hamstring tear at the Paris Diamond League meeting in early July, and his jump fell short of the 7.89m cut-off point.
With only three men reaching the automatic qualifying standard of 8.10m, the cut-off point to make Friday's final was reduced – a distance that Rutherford was agonisingly close to reaching.
Rutherford spoke to the BBC after the event: "The season wasn't going too badly up until Paris, when I ruptured a hamstring. I broke all the rules, really, in rehabbing quicker than I think anybody has in history from a ruptured hamstring.
"Training has been going really well and I woke up today and thought, 'This is going to be a good day'. But I knew after the final jump when I saw 7.87m come up that it wouldn't be enough and, even if it was enough, it's not really competitive. So I knew straight away."
Rutherford's failure was met with anger by fellow British long jumper Tomlinson, who took to Twitter to express his frustration having being overlooked for the World Championships to allow the injured Olympic champion to compete.
He wrote in a tweet, which was subsequently deleted: "Words can't describe my anger. Season ruined on media profile & not current athletic form. Thanks for the support from the athletics community."
Tomlinson later posted another tweet saying he needed to calm down in order to have a more measured reaction.
Rutherford responded to a social media backlash by telling his critics to "Imagine a picture of my bum hole. I'm waving it at you" and was adamant the selectors were still right to give him the thumbs up.
"That is definitely not the outcome I expected to say the least," he said. "It is gutting to come into something feeling great again, have all the expectations in the world and then not be good enough, that is ultimately what it comes down to.
"I just did everything I possibly could to be picked. I have jumped better this year [than Tomlinson] and I got myself fit again. As much as it wasn't a particularly great set of jumps I am not in pain so I can't be that badly injured at this moment in time.
"For both Chris and I there was a standard set and we should have jumped it. We are both good enough to jump 8.25m and we didn't do that this year. I felt for Chris and it would have been great to have us both at the worlds.
"But that has nothing to do with me if Chris makes it or doesn't, I just have to do what I have to do to make the championships. Ultimately I am still British No.1 as it stands, I have jumped further than him multiple times this year and I have beaten him nearly every time apart from where I got hurt.
"I think in any event if you are looking at somebody who has the better distance that year, won more head-to-heads and has a major title behind them it is a no brainer as to who should get selected.
"Chris is going to obviously be upset but there is nothing I can do about that. We were both in a bad situation having not jumped an A qualifier and that is what it comes down to.
"We both had plenty of opportunities and when speaking to Neil Black he gave us a two-week extension and he didn't give that to anyone else. We should have got the job done."