The attacking midfielder netted a brace at the Stadio Marc'Antonio Bentegodi to seal back-to-back wins for Filippo Inzaghi's side following victory over the hosts' city rivals Chievo before the international break.
With the two teams heading into the game level on 11 points, a visit to Verona was viewed as a stern test of Milan's recent revival under Inzaghi.
But the 18-time Italian champions were given early assistance as a spectacular own goal from Brazilian defender Rafael Marques put them ahead.
The triumph furthers Milan's UEFA Champions League credentials, which will be challenged again next week when they welcome Fiorentina to San Siro.
Verona appeared solid at the back in the early stages but conceded the initiative in unconventional fashion in the 21st minute when Marques volleyed Ignazio Abate's right-wing cross into his own net.
Japan playmaker Honda cruised into the box to latch on to Stephan El Shaarawy's pass and steer a cool finish into Rafael's bottom right-hand corner.
Andrea Mandorlini's Verona did carry a threat going forward, though, Luca Toni's spectacular overhead kick kept out by Christian Abbiati, who then denied Bosko Jankovic with a superb flying save down to his right.
Inzaghi's men looked to sit back and frustrate Verona in the second half and their task of seeing out the game was made easier in the 56th minute when Honda raced on to Adil Rami's long ball over the top to slot home Milan's third.
Lopez added a consolation three minutes from time before Verona were reduced to 10 when Marquez felled Giacomo Bonaventura.
However, that proved immaterial, with Milan's fine performance at both ends of the field boosting hopes that Inzaghi - who won two Serie A titles and Champions League crowns in 11 years as a player with the club - can return them to their former glory.
