Roberto Soldado gave the hosts a dream start when he volleyed home a corner in the sixth minute but Jose Maria Basanta’s equaliser 10 minutes before half time secured Fiorentina a draw and a crucial away goal.
The Italians will be favourites to make the last 16 ahead of next week’s return leg, particularly as Tottenham may have one eye on their Capital One Cup final against Chelsea three days later.
“It is a shame because at half-time we deserved to have scored more than one goal but it was only 1-1,” Pochettino said.
“We have 90 minutes in Florence to try and win the game and go to the next round. Today we were better than Fiorentina, especially in the first-half.
“We created a lot of chances but this is football. I think in the first half we controlled the game but we had more of the ball in the second-half.”
Despite voicing his disappointment with the result, Pochettino drew positives from the performance, adding: “In general, over the 90 minutes we were better. We had the chances, the possession of the ball and managed the game.
“It’s a shame and I’m disappointed with the result because I think we deserved more, but I’m happy with the performance.”
Pochettino opted to rest the likes of Harry Kane, Ryan Mason and Mousa Dembele against Fiorentina as Spurs enter a pivotal period that includes six games in 17 days.
Tottenham are sixth in the Barclays Premier League, only three points off the top four, and Pochettino admits he will have to juggle the team’s league and cup commitments in the coming weeks.
“Both competitions – the league and the Europa League – can give us access to the Champions League,” Pochettino added.
“We are fighting for the Europa League and in the Premier League. We try to focus on the next game and not think too much about the future.”
Pochettino added: “We need to make decisions because we have a lot of games coming up, six games in 17 days.
“It’s difficult and we need to rotate, give everyone the possibility to play. It’s not difficult to pick the starting 11, I try to select the best team to win the games.”