Leandro Trossard opened the scoring at the Emirates before Ben White and former Chelsea player Kai Havertz both scored twice in the second half to seal the north London club's biggest-ever win in the fixture.
The defeat came after Chelsea had gone eight matches unbeaten in the league, and dealt a blow to their hopes of claiming a European place next season.
"When we have bad days, we are so bad. When we are good, we are capable of everything," Pochettino told reporters.
"We cannot blame the players, I'm not going to blame the players. We cannot blame young guys who came here and after suffering some circumstances, come here to fight against a team preparing to win the Premier League.
"It is true we are disappointed with our performance, but I am not going to say something which is unfair to describe our team, our players, our squad."
Chelsea next face a trip to fourth-placed Aston Villa on Saturday, before hosting fifth-placed Tottenham Hotspur on May 2.
