Mr Javid said: "I've deleted a tweet which used the word "cower". I was expressing gratitude that the vaccines help us fight back as a society, but it was a poor choice of word and I sincerely apologise.
"Like many, I have lost loved ones to this awful virus and would never minimise its impact."
Before his apology, Covid-19 Bereaved Families for Justice joined opposition MPs in branding the remark insulting to people who have shielded and those who stayed at home to protect society.
Mr Javid said on Saturday he had made a "full recovery" and that his "symptoms were very mild, thanks to amazing vaccines", of which he had received two doses.
"Please, if you haven't yet, get your jab, as we learn to live with, rather than cower from, this virus," he wrote on Twitter.
Co-founder of Covid-19 Bereaved Families for Justice Jo Goodman said Mr Javid's comments were “deeply insensitive on a number of levels".
"Not only are they hurtful to bereaved families, implying our loved ones were too cowardly to fight the virus, but they insult all those still doing their best to protect others from the devastation this horrific virus can bring," she added.
"Words matter and the flippancy and carelessness of this comment has caused deep hurt and further muddied the waters of the Government's dangerously mixed messaging."
Shadow justice secretary David Lammy questioned his use of the word cower, in words echoed by Labour deputy leader Angela Rayner.
"129,000 Brits have died from Covid under your Government's watch," Mr Lammy wrote.
"Don't denigrate people for trying to keep themselves and their families safe."
Lib Dem health spokeswoman Munira Wilson said Mr Javid's tweet was "outrageous" while thousands remain in hospital with Covid-19.
"His careless words have insulted every man, woman and child who has followed the rules and stayed at home to protect others," she said in a statement.
"He owes them all, especially the millions who are shielding, an apology."
Public health expert Devi Sridhar said his remarks would be "painful to read for those who were severely ill" and those who lost loved ones to Covid-19.
The professor at the University of Edinburgh, wrote: "It wasn't because they were weak, just unnecessarily exposed to a virus.
"And wanting to avoid getting Covid isn't 'cowering' - it's being sensible & looking out for others."
Mr Javid received a positive test result on July 17 for a coronavirus infection that ultimately sent Prime Minister Boris Johnson and Chancellor Rishi Sunak into isolation as contacts.
Mr Johnson's quarantine in his Chequers country residence is expected to finish at the end of the day on Monday, as is Mr Sunak's.
The pair initially tried to avoid isolation by saying they were taking part in a testing pilot, but backed down in the face of widespread public criticism.
Mr Javid replaced Matt Hancock as Health Secretary last month when the scandal-hit predecessor stood down amid public outrage after leaked CCTV footage showed him kissing an aide in breach of coronavirus rules.
The successor has been seen as more strongly in favour of lifting coronavirus restrictions and most remaining legal rules in England were ended on Monday.