The mercurial Brazilian midfielder took advantage of referee Howard Webb's decision to award handball against Lubomir Michalik on 86 minutes.
And what made it even more annoying for Wanderers boss Gary Megson and his troops was the fact that they more than held their own against the Premiership high-flyers.
The hosts are bottom of the pile, but piled on the pressure after the spot-kick, as El Hadji Diouf hit the underside of the crossbar and City defender Michael Ball cleared off the line.
But visiting boss Eriksson will be absolutely delighted to have won this forgettable clash, in which both sides failed to test either keeper until the 63rd minute.
He will not care one jot that his side had to be patient, as he was only intent on wiping out the ghost of Saturday's 6-0 drubbing at Chelsea.
But for Megson, this will not have done anything to help his uneasy relationship with the home faithful, after he wasn't their chosen successor to Sammy Lee.
Eriksson made just two changes to his side that lost at Chelsea, opting to give his men the chance to redeem themselves.
His compatriot Andreas Isaksson replaced Joe Hart in goal - and Ball came in for toe injury victim Martin Petrov.
The visitors started slightly the better, but the hosts went close to breaking the deadlock with a shot from skipper Kevin Nolan that flew just over the bar. He then glanced header narrowly wide from Ivorian defender Abdoulaye Meite's cross just before the break.
The game only marginally livened up in the second half. Bolton's Stelios hit the target first when he forced Isaksson to make a save on 63 minutes and City's Richard Dunne worked Jussi Jaaskelainen three minutes later.
The 22-year-old Spanish full-back Javier Garrido was believed to be the main instigator of City's downfall at Stamford Bridge on Saturday, with the blame for five of the six goals attributed to him.
But Eriksson decided to push him up into left midfield at Bolton - although the move did not benefit either the individual or the team.
He was substituted ten minutes into the second half with Darius Vassell introduced to add more of an attacking threat.
In the end it just about worked, and Eriksson can now await Saturday's quarter-final draw.