The Lightning played their second game without two-time NHL scoring champion Steven Stamkos, who suffered a broken leg on Monday, and they have won them both.
Tampa Bay put just 20 shots on goal, but five of them got past Jonas Hiller while the division-leading Ducks were losing their second in a row. The Lightning won for the 14th time this season, most in the Eastern Conference.
Flippula opened the scoring with 8:08 to go in the first period and Martin St. Louis produced a power-play goal to give Tampa Bay a 2-0 lead after 20 minutes.
The Lightning doubled their lead in the second on scores from Flippula and Alex Killorn and Victor Hedman tacked on a Tampa Bay goal in the third.
Anaheim's lone tally came from Emerson Etem late in the second.
Ben Bishop collected the victory with 24 saves.