The Blaugrana looked set to register a fourth victory from four Group B matches when Malcom netted his first goal for the club seven minutes from time.
However, Mauro Icardi - otherwise anonymous as Inter struggled to trouble Barca - pounced to strike following a goalmouth scramble three minutes later, his goal crucial as Tottenham defeated PSV elsewhere.
Barca were still able to celebrate a place in the next round thanks to their superior head-to-head record against Inter, but this was a frustrating evening as they missed Lionel Messi's ruthless nature in the final third.
Ousmane Dembele drew an early stop from Samir Handanovic and Luis Suarez then curled one effort just over the top and sent a delicate lob wide, with Barcelona in control of proceedings from the off.
A sloppy start from Inter included a poor close-range Kwadwo Asamoah miss, but the majority of the chances continued to fall at the other end and Handanovic was again alert as the dangerous Suarez fizzed in a low strike shortly before half-time.
Handanovic turned away a Philippe Coutinho drive following the restart, before the goalkeeper blocked Ivan Rakitic's tame finish, with Suarez furious that his goal seconds later was in vain as the ball was ruled to have gone behind for a corner.
The breakthrough finally came just after Malcom's introduction in place of Dembele, charging through on the right to meet Coutinho's pass and shoot beyond Handanovic.
But Barca were denied the three points as Icardi finally saw a ball drop at his feet in the area, swivelling to bury the ball past Marc-Andre ter Stegen to the delirium of the home fans.
| FT Inter 1-1 Barcelona— Inter (@Inter_en) November 6, 2018
Late drama as that man @MauroIcardi gets on the #UCL scoresheet once again to help the Nerazzurri earn a positive point!! #ForzaInter #InterBarcelona #InterBarça pic.twitter.com/X1PFkB9a8J
What does it mean? Barca through but defensive worries persist
Barcelona wasted chance after chance. Icardi and Inter did not. The visitors looked Champions League contenders throughout the contest, yet they should have been able to see the game out. The Nerazzurri scarcely came forward but still managed to find a route back into the game, with confusion at the back for Barca. That should worry Ernesto Valverde going forward.
Coutinho controls second half
Artur was sublime in the first 45 minutes, patrolling the midfield, before compatriot Coutinho came to the fore after the break. Returning to former club Inter, his close control around the penalty area gave Milan Skriniar and his team-mates nightmares, before a brilliant break and pass teed up Malcom's strike.
Inter struggle to supply Icardi
Inter's chances were always going to be limited, but Icardi took the only one that came his way. The delivery to the Nerazzurri's main man was too often poor, with Sime Vrsaljko - so impressive at the World Cup - particularly wasteful when given time and space. Inter need their captain involved to make strides in this competition.
Key Opta Facts
- Barcelona drew their first UCL game without Messi since the 2006-2007 season: W15 L3 (83.3% of winnings).
- Malcom scored his first goal for Barcelona in all competitions with his first touch in his CL career.
- Gerard Pique has played his 100th CL game for Barcelona (including the two qualifying games vs Wisla in August 2008).