Pochettino's side were already eliminated from the Champions League before their last Group E fixture on Wednesday.
Pochettino's side were already eliminated from the Champions League before their last Group E fixture on Wednesday, but they rounded off a frustrating campaign with a dominant display against the Russian champions.
After a difficult period in which Tottenham suffered injuries to key players and lost their momentum as a result, Pochettino believes his men are back in the groove at a critical point of the season.
"We struggled in the last month and a half. We had some problems, but now we have nearly all the squad fit and we recovered that feeling we lost," Pochettino said.
"It's true it was a struggle to compete for a while. We crossed that period that was difficult for us.
"The team has full confidence and trust again. It's lucky that moment arrived in a very busy moment for us.
"Now we have an important period and we are arriving in good form."
Pochettino conceded it was frustrating to be the only English club knocked out of the Champions League in the group stage, but he took heart from Tottenham booking a place in the Europa League knockout stages by finishing third in their group.
Dele Alli got their equaliser after Alan Dzagoev's opener and Harry Kane put Tottenham ahead before an own goal by goalkeeper Igor Akinfeev sealed just their second European win this term.
Despite the potential for problems arising from the Europa League's gruelling itinerary and far-flung destinations, Pochettino is adamant Tottenham will treat the competition seriously because the winners qualify for the Champions League.
"The Europa League is not a consolation, it is an important competition. It is a trophy that is important in Europe," he said.
"You can qualify for the Champions League if you win it. The Europa league is a very good competition and why not believe we can win it."
Pochettino was also relieved Tottenham got their first win at Wembley since February 2008, ending a run of six games without a victory at the stadium that has been their temporary European home and is likely to be their home for the whole of next season while White Hart Lane is redeveloped.
"It's important to get a good feeling at Wembley. Now we need to look ahead. we have the opportunity to play more games here," he said.
"Yes we are disappointed we didn't get through in the Champions League but we were in a similar situation at this stage last season and finished strongly.
"In the Premier League we fight to go to the top and we are in a good position. The gap is not too much."
CSKA's failure to wrestle the Europa League spot from Tottenham was a downbeat end to the seven-year reign of boss Leonid Slutsky, who announced earlier in the week that he would resign after Wednesday's match.
Slutsky, who led CSKA to the Russian title last season, wasn't in a nostalgic mood and he said: "The only thing I can say is I feel disappointment. I can't talk about general things, just this game tonight.
"It was very hard. We had lots of missing players. I would say the result is fair against a very tough opponent."