Nigerian striker Peter Olayinka scored for Slavia Prague in the 63rd minute as the Czech side almost took all three points from San Siro.
Peter Olayinka became the first Nigerian to score on his Champions League debut since Yakubu’s hat-trick for Maccabi Haifa against Olympiakos 2002.
A stoppage-time equaliser was scored by Inter Milan substitute Nicolo Barella to deny Slavia Prague just their second Champions League group win.
The Czech side have reached the group stage for the second time but it was Stefan de Vrij and Danilo D’Ambrosio who went close for the Serie A leaders.
Yet Slavia deserved the lead when Peter Olayinka opened the scoring.
Barella bundled in after Stefano Sensi’s free-kick hit the crossbar, early in the eight minutes of added time.
Slavia goalkeeper Ondrej Kolar then produced a fine reflex save to keep out a Romelu Lukaku header right at the end, although the flag had already gone up for offside.
Three-time European champions Inter should have taken the lead from two Sensi free-kicks, with De Vrij heading over while fellow defender D’Ambrosio headed straight at Kolar.
Inter striker Lautaro Martinez also shot narrowly wide in the first half while keeper Samir Handanovic was fortunate to be awarded a free-kick after being caught in possession in his own six-yard box by Nigerian forward Olayinka, 23.
Kolar blocked a close-range shot by Martinez at the start of the second half, and Slavia replied as Nicolae Stanciu tested Handanovic with a 20-yard strike before firing over from a similar range.
The Czech champions then produced a fine move down the right, resulting in Olayinka cutting the ball back for Jaroslav Zeleny, and although Handanovic saved the substitute’s low shot at his near post, Olayinka fired the rebound into the roof of the net.
Lukas Masopust spurned a great chance to double Slavia’s lead as he fired over and Inter barely threatened a leveller until on-loan Cagliari midfielder Barella, 22, volleyed into the ground and the ball somehow bounced through a crowd of bodies and into the Slavia net.