The Blues had to wait until the final kick of the game to seal their progress to the last 16.
Substitute Eden Hazard's stunning stoppage-time strike secured a 1-1 draw that eventually saw of Sparta Prague's persistence.
But the Czechs left west London feeling as though they had missed their chance to pull off a shock after David Lafata had equalised on 17 minutes.
While Chelsea dominated possession thereafter, Rafael Benitez's side lacked a convincing cutting edge - highlighted by misfiring striker Fernando Torres.
The Spaniard missed four clear-cut chances to stretch a barren run that has seen him score just once in his past 14 appearances.
Torres' profligacy perhaps should have been punished in full as Sparta, a constant menace on the break, wasted their own chances late on to send Chelsea out of a sixth competition this season.
Bertrand, however, remained convinced his side would eventually find the telling blow to set up a clash with Steaua Bucharest in the next round.
"I never thought that we would lose," he said.
"I always felt quite confident we were going to get (an equaliser), it was just a matter of when.
"I think we started well and their goal came as a surprise to many of us.
"We were saying on the pitch: 'forget about that now and move on'.
"We were confident enough that we could get the result, which we did, although we left it late."
While Torres' latest blooper reel of misses grabbed the headlines, Chelsea's susceptibility to counter-attacks offered further reason for frustration around Stamford Bridge.
After Gary Cahill had been turned inside out in the box before the opener he and defensive partner John Terry were more than once forced into saving tackles to spare the home side's blushes.
"They hit is a few times on the counter-attack," Bertrand said.
"We were on top for nearly all of the second half, it was making sure we didn't let them get that second sucker punch.
"We had to make sure we concentrated and nullified that threat.
"Then, thankfully, Eden came on and showed us what he can do."
Hazard had replaced Oscar on 67 minutes - which was welcomed by boos from a home contingent who had expected Torres might instead get the hook - but Benitez's decision was vindicated in the end.
Hazard was a £32million buy from Lille in the summer and he showed what that sort of money should buy with a piercing bit of skill to settle the contest.
"It was a fantastic goal. He is some player," Bertrand said.
"It comes as no surprise to us. It was a fantastic goal and a fantastic display from him personally."
The 2-1 aggregate success sets up another trip to eastern Europe in the next round after Steaua overcame a 2-0 deficit to beat Ajax on penalties in the Romanian capital on Thursday night.
"That will be a tough proposition," Bertrand said.
"For them to take a 2-0 deficit back home and overturn that proves that it will be a hard place to go to.
"A club like Chelsea expects silverware. We expect that year in, year out so we'll try our best."
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