After a lively opening half hour the Portuguese forward, scorer of a record 121 Champions League goals, was involved in a tangle in the penalty area with Valencia defender Jeison Murillo as he awaited a cross from the left.
Cristiano Ronaldo was sent off in the 29th minute of his first Champions League match with Juventus on an absurdly soft call.
The 33-year-old appeared to knock Murillo off balance before briefly grabbing the Colombian's hair.
Ronaldo broke down in tears after the German ref made a decision to send him off when he put his hand on Valencia defender Jeison Murillo's head.
Ronaldo looked baffled and kept protesting his innocence, briefly laying on the ground to express his disbelief. "He needs to rise above it and focus on Sunday, even if these things leave a bitter taste in the mouth".
"I didn't see the contact, I was affected by his tears".More news: Strong winds but warmer weather ahead as ex-hurricane Helene hits
"We will play Young Boys at home and in theory we should defeat them", Allegri said. "I spoke with him but I won't say what I told him".
Bale nearly increased Madrid's lead with a close-range shot that struck the crossbar early in the second half but the Wales forward did make it 2-0 in the 58th with a well-placed low shot after a superb through ball from Luka Modric.
Ronaldo started brightly, with an ambitious shot from distance, and then had a hand in teeing up two glorious chances.
The Bianconeri have won the Serie A title for the last seven seasons - and the league and Italian Cup double for the past four - but have struggled to transfer that domestic supremacy to the European stage, although they have reached the final twice in the past four editions.
Lopetegui again refused to answer who his first-choice goalkeeper was and whether Keylor Navas, who had two strong saves in the match, would be the keeper for the entirety of the Champions League.
Cristiano Ronaldo's sister, Katia Aveiro, has come out in defence of him after his red card.
Despite their numerical advantage, Valencia walked away from a packed Mestalla empty-handed following a pair of Miralem Pjanic penalties.