Jose Mourinho introduced both Paul Pogba and Zlatan Ibrahimovic in the second half and the pair combined to hit the winning goal late in the game.
The Welshman made a triumphant return after three months on the sidelines to sign off a routine victory for the hosts on Saturday.
The European champions got off to a bad start at the Santiago Bernabeu, but responded well with goals from Karim Benzema, Toni Kroos and Casemiro.
Luis Enrique's men were comprehensively outplayed at Parc des Princes and now need a miracle to reach the quarter finals.
Whatever is decided about the Blues' second goal in the 2-0 win at Bournemouth, Pep Guardiola wants more from the Argentine.
The Blues opened the scoring through Pedro but the Republic of Ireland winger levelled the affair with a beautiful free-kick.
The Gunners scraped to victory over the struggling Tigers, though the Chilean attacker benefited from the ball hitting his arm and going in.
The Italian champions are now seven points ahead of second-place Roma following their win over struggling Crotone on Wednesday.