A much-changed Spurs side closed their Group B campaign with a 3-1 defeat at Bayern Munich in a game where nothing was at stake.
Mourinho's men will now face Barcelona, Juventus, Paris Saint-Germain, Valencia or RB Leipzig in the next round, with the draw taking place on Monday.
The Portuguese said by the time the last-16 encounters come around in February, his side will be a force to be reckoned with.
"I think from the teams that finished second, I think the teams that finished first will wish they don't play against us," Mourinho said.
"We are one of the strongest teams from the second group. I know we are a country that goes through a crazy period which many, many times leaves marks on players and teams and conditions, but by the end of February I will understand my players better, they will understand me better.
"We have two more months of work together. I think so, we will be much more ready. But today was not a question of being or not being ready."
Mourinho is in a much more informed position after giving his fringe players a chance at Allianz Arena, with nothing at stake.
Ryan Sessegnon, Giovani Lo Celso, Juan Foyth and Kyle Walker-Peters all made their first starts under the new boss and it was Sessegnon who impressed the most, scoring Spurs' goal.
They ultimately went down to a 3-1 loss, with Kingsley Coman, Thomas Muller and Philippe Coutinho scoring for Bayern, but Mourinho is pleased to be now armed with information.
Spurs can now switch their focus back to domestic matters, as the north London outfit prepare to travel to Wolves in the Premier League on Sunday.