La Russa commented during a televised interview that home-plate umpire Jerry Meals had "two different strike zones" for the two starting pitchers from St. Louis and Philadelphia.
"I have no disagreement at all," La Russa told his team's website (stlouis.cardinals.mlb.com), of the undisclosed fine.
"As soon as MLB called, my response was, 'Whatever is imposed, you'll get no argument.'
"If I get a chance, I will apologize to Jerry. We were competing, and I got upset and crossed the line."
The Cardinals rallied to beat the Phillies on Sunday before losing 3-2 on Tuesday, and now trail Philadelphia in the best-of-five series 2-1.
(Writing by Jahmal Corner in Los Angeles; Editing by Ian Ransom)