With the tie evenly poised after a 1-1 draw in Portugal in the first leg, the Blues started brightly with Andriy Shevchenko thundering an effort over from 30 yards out on the left.
The game then settled into a low-key midfield battle, before the visitors silenced most of Stamford Bridge with a superb breakaway goal after 15 minutes.
Lisandro Lopez fed Lucho Gonzalez in midfield and his superbly weighted throughball allowed Ricardo Quaresma to sprint clear and fire his shot under the advancing Petr Cech.
That setback clearly upset Chelsea's rhythm and it took them until the half-hour mark to fashion an opening.
Michael Ballack looked set to score from eight yards out, but Ricardo Costa got in superbly to clear the danger after another Ashley Cole cross.
However, the rest of the first period saw Porto stand firm and offer the Blues few opportunities to worry keeper Helton.
Jose Mourinho brought on John Obi Mikel for Claude Makelele and the change paid dividends three minutes in as Arjen Robben found space 30 yards out and fired in a left-foot shot which Helton fumbled into the back of the net.
That brought a total change in the flow of play, with the Blues starting to impose themselves on their opposition.
Twenty minutes from time Ricardo Carvalho headed over after Frank Lampard's free-kick caused all sorts of problems in the Porto area.
Nine minutes later Chelsea struck the decisive blow as Cole's deep ball into the area was nodded on by Didier Drogba to Shevchenko, he cushioned a header down to Ballack and the German drilled a left-foot shot into the corner of the net from eight yards.
From that point Porto were beaten and they didn't extend Cech in the closing minutes, while at the other end Lampard almost set up substitute Salomon Kalou for a clincher.
Soon after the final whistle brought relief to most of Stamford Bridge as Chelsea progressed to the last eight of the competition.