The Blues progressed to the fifth round after Kepa Arrizabalaga's penalty heroics helped them beat the Pilgrims in extra-time.
The Spain goalkeeper guessed correctly and smothered Ryan Hardie's last-gasp spot-kick, after the Plymouth striker had been felled by Malang Sarr.
Marcos Alonso thought he had settled the tie with a neat finish in extra-time, only for Argyle to battle back and force one more opening.
Kepa kept his cool to conjure a fine save however, on a day where Chelsea markedly missed Thomas Tuchel after the Blues head coach tested positive for Covid-19.
Nevertheless, the Blues - who are preparing to travel to Abu Dhabi for the Club World Cup - got the job done over the League One side.
And Michaels, stepping in for Tuchel, said he was relieved that they managed to get the win eventually after creating so many chances.
"We were happy until the 60th minute we have to say," he told talkSPORT.
"We created a lot of opportunities and chances, at the end I think we had 40 shots.
"We lacked a bit of precision from crosses on the side and passes in the box.
"We didn't do ourselves a favour at 1-0 down and then there's a penalty.
"Everybody believes it's easy to play this game but it isn't in FA Cup and we saw this yesterday also.
"They were well organised, they guarded their box but at the end, we are through."
Michaels also spoke about Romelu Lukaku, who struggled to make his mark in the game once again.
"He's working a lot for the team, doing lots of touches, but is a little bit unlucky.," he added.
"We try to put him, give him opportunities and we will keep on going like this because he is an important player for us.
"He is our striker so he also needs some trust in moments he doesn't score."