Arsenal led early on through Aaron Ramsey's well-taken goal, but Harry Kane's contentious penalty 16 minutes from time ensured third-placed Spurs maintain a four-point lead over the Gunners in the fight for top-four finish.
Unai Emery's men will reflect on a missed opportunity to inflict further pain on a Spurs side that had lost to Burnley and Chelsea in the past week, particularly after Aubameyang spurned the chance to win the game twice over in the dying seconds.
The Gabon striker's weak penalty was saved by Lloris before Jan Vertonghen produced a stunning last-ditch challenge to prevent Aubameyang turning home a follow-up effort.
Lloris was criticised for his role in both of Chelsea's goals in a 2-0 win on Wednesday, but Pochettino insisted he never doubted his captain.
"Lloris' save was a massive present. I am so happy because we didn't deserve to lose the game -- we were better than them so it would be a shame to lose the game in that way," said Pochettino.
"The whole team had a bad night on Wednesday, not Hugo. You put the finger on Hugo, but he was not responsible for the defeat.
"When defeats appear it is normal, players like Hugo or if Harry misses some chances, it is normal the spotlight is on them because they are so big players."
Aubameyang left out
Emery made a number of big calls with his starting line-up with top-scorer Aubameyang dropped to the bench in favour of Alexandre Lacazette.
The Frenchman spurned a great chance inside three minutes when he skewed his shot wide with just international teammate Lloris to beat.
However, he made amends with a great pass to free Ramsey on 16 minutes.
The Welshman has already signed a pre-contract deal to join Juventus next season, but at the stadium where he scored the winner in two FA Cup finals for the Gunners, he left the Arsenal support with another memory to cherish by coolly rounding Lloris before slotting into the empty net.
Spurs started like a side short on confidence, but they slowly wrestled back control of the game towards half-time and were only denied by a fine double save from Bernd Leno.
Kane's scooped pass picked out Christian Eriksen who shot too close to the advancing Leno before the German goalkeeper then made a remarkable stop to turn Moussa Sissoko's follow-up effort behind.
Lacazette passed up another big chance at the start of the second period when he again failed to hit the target at the end of a well-worked Arsenal move before being hooked for Aubameyang just before the hour mark.
Yet, it is at the other end of the field Emery still has more work to do as Arsenal remain without a clean sheet away from home in the Premier League this season, although there was plenty of controversy about Spurs' equaliser.
Shkodran Mustafi was guilty of a push on Kane's back, but the England captain should have been flagged offside before referee Anthony Taylor pointed to the spot.
"For me today the referees had a big personality, but it is not enough to make the best decisions in difficult actions in the box for them and for us," said Emery. "VAR is coming to help them."
Kane dusted himself down and slotted home his 22nd goal of the season.
Aubameyang's failure to do the same thing meant Spurs drew for the first time in the league this campaign to remain in the driving seat for Champions League football next season, before Arsenal midfielder Lucas Torreira was shown a straight red card with seconds left for a lunge on Danny Rose.