"We are still improving and can get better for sure," Chelsea captain John Terry said. "It was important for us to top the group tonight. Some tough teams have topped the groups."
By securing top spot ahead of Schalke, Chelsea, which won the Europa League last season, will play one of the group runners-up in the round of 16.
With Chelsea unable to face Schalke or an English rival, AC Milan, Bayer Leverkusen, Olympiakos, Zenit St. Petersburg and Galatasaray are the potential opponents in Monday's draw.
However tough it could be facing Galatasaray, Mourinho wants former Chelsea striker Didier Drogba to get the chance to return to west London with the Turkish champions.
"Galatasaray is very difficult but I would like Didier to come back here and feel what I felt (returning)," Mourinho said.
Chelsea's defense proved to be sturdier in Europe again on Wednesday, in contrast to its domestic showing.
This was Chelsea's fourth clean sheet in six Group E matches, with the only goals conceded to Basel.
In the Premier League, though, the Blues have conceded 17 goals already, two more than in the whole of Jose Mourinho's first season in charge 2004-05 when they won the 2004-05 title.
Chelsea's misfiring strikers have been as much of a concern for Mourinho, and Ba's effort against Steaua was initially given as an own goal.
Oscar headed the ball across goal and it appeared that Daniel Georgievski flicked the ball into the net, but it was later ruled that Ba did get the final touch.
As rare as Ba finding the net was Mark Schwarzer appearing in the Chelsea goal, with the Australian making his Champions League debut at 41 in his first season with the club.
Not that Schwarzer could prove himself against a side that offered little attacking threat.
Just after Ba's opener, Gabriel Iancu sent the ball wide for the visitors and a cross from Georgievski was easily collected by Schwarzer.
A second goal proved elusive for Chelsea.
Branislav Ivanovic header from Eden Hazard's cross was turned over by Ciprian Tatarusanu.
The goalkeeper intervened to prevent Ba scoring again as he attempted an overhead kick after controlling the ball with his chest.
"We don't have enough patience sometimes to pass the ball and wait for spaces," said Mourinho, who has won the Champions League with Porto and Inter Milan.
At start of second half, Ba's final touch let him down when he blazed over from six yards after getting on the end of William's cross.
And, after Hazard headed over, Ba found the net again in the closing minutes only for the effort to be ruled out for offside.
"At the end of the game I was really tired," Ba said. "I need to work on my fitness."
Chelsea is back in the round of 16 after being knocked out at the group stage last season under Rafa Benitez.
"We had one target not to win the Europa league again," Mourinho said. "And that target is done."