With Leverkusen facing strugglers Freiburg on Sunday, Bayern expect to lose their status as league leaders before the end of the weekend, but van Gaal was delighted with his side's effort.
Goals by Daniel van Buyten, Mario Gomez and Arjen Robben gave Bayern the three points in difficult conditions as heavy snow fell throughout the game.
"We have see our best home performance here today," said van Gaal. "I think Mainz are not an easy team to beat, they have a goalkeeper who can normally stop any ball.
"He made a mistake in the second half and we benefited from it, we created so many chances and had their goalkeeper under pressure.
"We played well against a defensive side and I am very pleased we have seen some good goals as part of a good performance from Bayern."
Dutch winger Robben scored his second goal in two matches to seal Bayern's seventh successive league win.
Having scored the winner in the 3-2 win at Bremen the week before, Robben curled in another free-kick with time running out to underline his status as a dead-ball specialist.
"The weather was not good, it was the same for both sides, but it worked out for us," said Robben after the ball had slipped out of the Mainz goalkeeper's hands for the first Bayern goal.
"We were lucky with the first goal and things went well after that. The coach told us to stay calm at the break because we were still level and our patience paid off."
And fellow goal-scorer van Buyten said it was important for Bayern to stay in the winning habit as they looked to keep the pressure on Leverkusen. "It was very important that we got the win to make sure we stay motivated," said van Buyten who scored his fifth league goal of the season.
"We still have many games to go this season and Leverkusen are a good team who play good football," the Belgian added. "It will get tougher the closer we get to the end of the season. We will give our all to the end of the season and then we will see which team is top of the table."