Hibs were hammered 10-1 on aggregate by Bayern Munich, while City lost 3-1 to Eskilstuna United from Sweden.
"I think it is fantastic for Scottish football that we actually have two teams in the Champions League," Signeul told BBC Scotland.
"It just shows that what we have done has actually brought us two spots."
Signeul pointed out that the Netherlands, who will host the Euro 2017 finals and play Scotland in a 20 October friendly in Livingston, only have one team in Europe's top club competition.
"It is all based on rankings and what Glasgow City and the national team have done previously," she pointed out.
Hibs were making their debut in the knockout stage.
"It was a great experience for this young Hibs team and they were unlucky in the draw - played probably one of the challengers for the title this year, Bayern Munich, with 26 players in the squad all full-time professionals and all playing for their national squads; Austrians, Swiss, Germans, Dutch," Signeul stressed.
"Bayern Munich also had the golden boot player of the tournament in the Olympics, so it was a tough side.
"It is good for all the players at Hibs to see this is the level they want to get to.
"Sometimes you play in internationals and get a little bit cheated - you think you are better than you are because you are playing weaker teams."
City, Scottish champions for the last nine seasons, reached the Champions League quarter-finals in 2014 but have suffered disappointment two seasons in a row in the round of 32.
"Glasgow City had a chance in their game, but Eskilstuna, the Swedish runners-up, were a little too strong for them," said Signeul.
"They had two good games and they were a little unlucky in the way the goals came in both games."
The future of Signeul's Scottish FA colleague, men's head coach Gordon Strachan, was called into question this week after a draw with Lithuania and a defeat by Slovakia in their 2018 World Cup qualifiers.
Signeul stressed that it was unfair to compare the success of her side to Strachan's because "results usually follow the rankings in women's football" while the men's game was more competitive and less predictable.
She added that she believed Strachan, who has decided to remain in post, continues to have the full backing of his players.
Scotland boss Anna Signeul remains positive despite Glasgow City and Hibernian going out of the Women's Champions League this week.