Ursula von der Leyen said there had been “more movement” on problematic issues after “difficult weeks with very, very slow progress”.
But she warned there were “some metres to the finish line” to reach agreement.
It comes as negotiations moved online after a positive Covid result among the EU team.
Face-to-face talks between the two sides in Brussels were suspended on Thursday after the test result in the team of EU chief negotiator Michel Barnier.
The two sides are racing to strike a deal to govern their trading relationship once the UK’s post-Brexit transition period ends in January 2021.
Negotiations will continue via video link on Friday and over the weekend, as the two sides work out when in-person discussions will be able to resume.
BBC Brussels correspondent Nick Beake said he had been told Mr Barnier would now self-quarantine following the team member’s test result.
But it was understood no members of the UK team would be required to self-isolate, our correspondent added.
‘Three main issues’
Speaking to reporters in Brussels ahead of this weekend’s virtual G20 summit hosted by Saudi Arabia, Mrs von der Leyen said “time pressure is high” to reach a deal.
But she added that negotiators would have “substance” to discuss during video conferences because legal text for a deal was on the table.
“After difficult weeks with very, very slow progress now we have seen in the last days better progress, more movement on important files. This is good.”