Cowan scored in the first and third periods to run his goal streak to five in three games after ending a 52-game goalless drought.
Kevin Bieksa, Daniel Sedin and Bryan Smolinski, picked up at the trading deadline, also scored for Vancouver as the Canucks continued their domination of Eastern Conference teams with their eighth win in 10 games.
Sedin reached the 30-goal plateau for the first time in his career as Vancouver clinched the win with three third-period goals.
Vincent Lecavalier scored on Vancouver netminder Roberto Luongo, who tied the franchise record of 38 wins by a goalie set in 1991-92 by Kirk McLean.
Luongo, once tested 50 times by Tampa Bay when he played for Florida, faced only 17 shots as the sellout crowd celebrated his saves with shouts of “Lu-u-u-u”.
The Canucks (39-22-5) won their third straight game to continue a run that has seen them go 22-4-4 since Christmas. The result left them two points ahead of the second-place Calgary Flames and four clear of the Minnesota Wild in the Northwest Division.
The Lightning lost their second straight game and third in their last four to fall to 37-27-4 and into second place, two points behind the Atlanta Thrashers in the Southeast Division.
Sedin gave Vancouver breathing room when he found brother Henrik Sedin’s pass on Johan Holmqvist’s doorstep and tucked it behind the goalie 21 seconds into the third period.
Smolinski scored his first goal as a Canuck after Vancouver killed the first penalty of a 1:01 two-man advantage. Holmqvist mishandled the puck and Smolinski put it between his legs.
Vancouver nursed a 2-1 advantage after Bieksa, the young defenceman who leads the Canucks in ice time, broke to the net to take a behind-the-back pass from Daniel Sedin.
He chipped the puck behind goalie Holmqvist for his 11th goal of the season and third in seven games.
Holmqvist kept his team close with a pad save on Markus Naslund then got a glove on a Lukas Krajicek blast before foiling Matt Cooke and Cowan in the final seconds of the middle frame.
He then outguessed Jan Bulis with a glove save in the third.
Cowan, the hard-nosed waiver wire pickup who has turned into a scoring machine, got the only goal of a first period that saw both teams combine for a sparse six shots on net. Brendan Morrison left his zone with enough speed to get around defenceman Shane O’Brien and leave the puck at the edge of the crease for Cowan.
The Lightning tied the game with their fifth shot of the game 26:51 after the opening face-off when Vancouver’s No. 1-ranked penalty kill gave up a goal for the eighth straight game. Lecavalier floated the puck over Luongo’s shoulder for his league-leading 44th goal of the season after the Canucks surrendered their third straight power play.
NOTES:Tampa Bay is the third-least penalized team in the league, averaging 10.8 minutes a game … the Lightning continue their season-high six-game road trip Wednesday night in Edmonton … Tampa Bay and Vancouver met for the first time in three years … the Canucks won the last contest 5-4 in overtime when Markus Naslund had two goals and two assists.