The Greek striker, making his first appearance of the season, struck a dramatic last-minute goal to end the spirited display from Championship club Norwich City.
With extra time beckoning at Eastlands, Samaras struck the decisive blow after racing on to a through ball from substitute Kelvin Etuhu to slot home the match-winning goal.
The strike from Samaras was the highlight of a dour clash involving two weakened sides.
City made nine changes from the side that drew 3-3 at Fulham in the Premier League three days earlier, with Richard Dunne and Stephen Ireland the sole survivors from that line-up.
It was a similar story to the previous round when City brought in eight players at Bristol City where they also triumphed.
Norwich were also without nine senior players, those these were enforced through injury and suspension as manager Peter Grant was down to his last 16 available players .
Canaries keeper David Marshall made an excellent early save to keep out a free-kick from Michael Ball.
And young City keeper Joe Hart also showed why he is an England Under-21 international after making an equally good stop to keep out a free-kick from Jon Otsemobor.
They were the only clear-cut chances of a disappointing first half in which City lacked a cutting edge after creating a number of promising openings.
The second half remained lacklustre and in desperation City manager Sven-Goran Eriksson sent on young front players Etuhu and Ched Evans for their first team debuts.
And it was 19-year-old Etuhu who set up the winning goal for Samaras to score.
City might have doubled their margin of victory deep into stoppage time when Samaras turned provider to release Rolando Bianchi, who burst through on goal only to see Marshall make a brilliant block with his legs.
Afterwards Eriksson explained that he remains undecided as to whether to field further weakened teams in the competition as he expressed a desire to be successful in both the Carling and FA Cups.
There is an enormous wait of expectancy for Eriksson to deliver silverware having spent £40million on a new-look side with and City's last honour coming 31 years ago.