Jonas had levelled the tie for the visitors with a second-half strike, before Ezequiel Lavezzi restored parity minutes later, as an under-performing French outfit limped into the last eight for the first time since 1994-95.
The Italian trainer maintained that while his side was not at its best, it had done well in the competition so far.
"It was very hard, a very difficult game. They [Valencia] played really well. We were not at our best in the first half," the 53-year-old told Sky Sports.
"After we conceded the goal, we did better. It's a very important result for the club, to reach the quarterfinals after 18 years is very important.
"The goal we conceded woke us up. We were controlled too much in the first half. It's very difficult for us to win [the Champions League], but it's our aim to do our best. At the start, everyone said the team didn't know what they were going to do, but we won the group, won the last 16, and we hope to do well in the quarterfinal."
Midfielder Blaise Matuidi also echoed his coach's words, but insisted that the team can be proud of its achievement and vowed to fight to reach the semifinals.
"It's great but it's true that we fought like dogs for that. We have done something great and now anything can happen," the 25-year-old told reporters after the match.
"We have done something great, and now anything can happen. We are still in three competitions (the Champions League, Ligue 1 and Coupe de France), which many people tend to forget. We showed we're in the mix. We will fight until the end."