Pedro Leon struck the all-important equaliser for the visitors deep into stoppage time after fellow substitute Filippo Inzaghi had netted two trademark poacher's goals to turn the game following Gonzalo Higuain's effort on half-time.
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"It was a goal that gave us great satisfaction, it was good for Pedro Leon but great for the team because we still haven't lost and we are through," Mourinho told a news conference with little apparent sentiment for his former surroundings.
The charismatic Portuguese led Inter Milan - who share the San Siro as a ground with AC Milan - to the European Cup and an unprecedented Italian treble last term and was determined to remind rival Milan supporters as he made the provocative fingered gesture on the bus arriving for the Group G game.
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His first return to the famous stadium since leaving Inter in May started with an enormous explosion of whistles from the 75,000 Milan fans when his name was read out over the speakers.
His appearance from the tunnel sparked a volley of obscene chants but the livid Rossoneri faithful were soon silenced as classy Real took charge and went ahead when Higuain found a vast hole in the Milan's defence to finish off Angel Di Maria's pass.
EVERGREEN STRIKER
Milan, who meekly lost 2-0 at the Bernabeu two weeks ago, were thoroughly second best but the introduction of 37-year-old Inzaghi completely changed the game.
The evergreen striker, little used these days, nodded in after Iker Casillas flapped at Zlatan Ibrahimovic's cross on 68 minutes and he prodded in his second 10 minutes later although Mourinho was adamant he was offside.
"Inzaghi is important because at 37 he always has enthusiasm and he encourages the young players," Milan coach Massimilano Allegri said.
Real have never won at the San Siro but it almost felt like a win to them when Pedro Leon appeared from nowhere to score.
Mourinho had the last laugh over the Milan fans as he waved his arms about in delight and stuck his tongue out before remembering the game was not yet over and quickly grabbing substitute Raul Albiol to tell him to go on with seconds left.
Auxerre's win over Ajax in the other group game meant the draw was enough to seal Real's passage into February's first knockout round, where they have lost for the last six seasons.
Their chances of progressing beyond that stage this term look high given Mourinho's immense skill and pedigree and the fact he desperately wants to become the first coach to win the European Cup with three different teams - he also triumphed with Porto in 2004 - as early as possible.
Second-placed Milan's future under novice former Cagliari coach Allegri is less clear but a trip to Auxerre and a final home game against Ajax should herald qualification despite striker Alexandre Pato's woeful form.
Ibrahimovic's inability to make a major impression in the big matches also continues to undermine his enormous talent.
Real's Cristiano Ronaldo was also not at his best and went down theatrically clutching his face after a minor
