The 61-year-old TV presenter – who is suffering intense pain in his pelvis - was hosting the ITV daytime show with wife Ruth Langsford - leaving her to explain his absence from screen.
Langsford, 61, told viewers following an advert break: "Hello, welcome back to This Morning, now those of you who follow Eamonn on social media will know he has been talking a lot about chronic pain.
"And it's ironic now that he is not here, because he's had to nip to the loo, because it takes him so long walking and he is on his way back.
Watch: Eamonn Holmes thinks social media trolls plotted his This Morning axe
"He is here any minute, there he is - it takes him longer to walk, but he is here now."
Holmes hobbled across the studio to rejoin his wife for the segment discussing Line Of Duty character DS Steve Arnott's who has a painkiller addiction in the programme.
Former GMTV presenter Holmes has been documenting his battle with chronic pain and subsequent insomnia on social media – and has now revealed he has resorted to taking cold showers in a bid to ease his suffering.
He tweeted: "Physio just left after 2nd session of the day . He said my body was hot ... result being that I Needed to cool off with my 2nd Cold Shower of the day.....Let's hope it helps me sleep soundly Zzzzź."
Holmes had to get up early to undergo his first physiotherapy session at 4.30am before hosting the This Morning with Langsford for the Easter holidays.
He told viewers: "Those of you who follow me on social media will know, about a month ago I did something to my back, I don't know how I did it, getting into the car, getting out of a car, getting out of bed, whatever.
"I've got an MRI scan, but the trouble is, everything closes for Easter, I haven't got it analysed yet, but what I do know is, I can't sleep at night.
"The pain is absolutely worse at night, the humbling thing is when you go on social media and you talk to people who suffer from this, age isn’t a barrier, where you live isn't a barrier, how much you earn isn’t a barrier."
A spokesman for Holmes previously told Yahoo! UK: "A month ago his pelvis went out of line so he needs physio most days as the pain is intense."
The TV presenter underwent a double hip replacement in 2016. The surgery was carried out in a bid to tackle excruciating hip, leg and back pain he had secretly suffered for more than 20 years.
Watch: Ruth Langsford on her marriage to Eamonn Holmes