Sidney Crosby, Maxime Talbot and Ryan Whitney for the Penguins scored for Pittsburgh, while Antoine Vermette, Daniel Alfredsson and Wade Redden scored for Ottawa.
The victory gives each team 92 points, with Ottawa having one more victory and the Penguins holding a game in hand.
Using his backhand, Ruutu tucked the puck past Ottawa goalie Ray Emery as the second Penguins shooter in the shootout. Ruutu was used in the shootout for only the second time this season since replacing Evgeni Malkin in that role last week. He is now 3-for-6 in the shootout.
Penguins goalie Marc-Andre Fleury stopped Mike Comrie, Dean McAmmond and Vermette to improve to 9-5 in shootouts this season.
Pittsburgh was on its way to its fifth win in a row, holding a 3-2 lead with a two-man advantage with seven minutes left.
But after killing off 56 seconds of a Pittsburgh five-on-three, the Senators got a holding the stick penalty called on Malkin.
After playing 65 seconds four-on-four, Redden scored his seventh goal of the season a second after the power play began.
Fleury did not see Redden's shot from the point until it went between his legs.
Five of the past eight Penguins games have been decided in a shootout - including a 5-4 Pittsburgh win in Ottawa 12 days ago.
Crosby and Whitney had a goal and an assist for the Penguins, who have won five in a row, are 7-0-1 in their past eight and moved within two points of the New Jersey Devils for the Atlantic Division lead.
The Senators are 4-0-4 in their past eight games and 12-1-5 in their past 18.
Talbot scored the game's first goal 10:44 into the first period off a short-handed rush that featured precise passing by Colby Armstrong and Sergei Gonchar to feed Talbot for his 11th goal of the season.
The Senators tied the game 26 seconds later when Vermette scored his 18th on assists from Chris Kelly and Chris Neil.
Crosby had a power-play goal four minutes into the second when he corralled a pass from Whitney that may have been intended for Mark Recchi, turned it over to his backhand and beat Emery for his 32nd of the season.
Ottawa tied it again. Alfredsson deflected a Joe Corvo shot from the point past Fleury. Alfredsson's 26th came 61 seconds after Crosby's goal.
Whitney gave Pittsburgh its third lead with 2:55 to play in the second. His 11th goal came partially as a result of Crosby holding onto the puck and working the far boards while on the power play.
Crosby, who extended his league scoring lead to 12 points, has five goals and five assists in his past six games.
Notes: Gonchar had two assists. ... Recchi has gone 13 games without a goal - the longest stretch of his career while in a Penguins' uniform. ... Corvo has four points in his past three games. ... The Penguins will play their fifth game in seven days Monday night in New York against the Rangers.