Both teams were desperate for points as the race for Europe reached its climax.
Everton went for an attacking 4-4-2, with David Moyes not wanting to go to Chelsea on the last day of the season needing points to qualify.
Harry Redknapp stated before the game that he would be happy with a point, but with his Portsmouth side facing Arsenal in the last game, he would have been hoping to leave Merseyside with a full quota.
Youngsters Victor Anichebe and James Vaughan, who committed their long-term futures to Everton this week, were paired together for the first time as the Toffees went for broke.
The home side started brightly enough without displaying any real threat while a comfortable Pompey defence were happy to cut-out midfield to play long balls to Nwankwo Kanu and Benjani Mwaruwari.
However, as the game progressed Gary O'Neil and Lauren began playing probing balls that found Everton looking decidedly shaky.
One period of Portsmouth pressure saw Everton concede three corners and escape only when Djimi Traore headed wide to hand the home side possession.
In the 27th minute though, Everton's nerves should have been settled when a neat back-header from Anichebe found Vaughan. But with only David James to beat the teenager screwed his shot wide of a gaping goal.
Despite a flurry of corners for Everton and chances for Anichebe and Joleon Lescott just before half-time both sides went in goalless after a dire first 45.
The Blues missed another clear-cut opportunity just after the break, Mikel Arteta drilled in a low cross which by-passed intended recipient Leon Osman but fell to Lee Carsley six yards out. The Irish international only succeeded in blasting his shot inches wide under little pressure.
The home side were finally stepping up the pace though and minutes later Osman just failed to get on the end of a Phil Neville cross as Portsmouth began to look rattled.
Anichebe and Vaughan combined to win Everton a penalty after Glen Johnson hacked Vaughan down in the 60th minute after a clear run on goal.
Arteta stroked the ball home to give the Toffees a just about deserved lead.
Minutes later an unmarked Joseph Yobo made it two after powering a header past James from an Arteta corner as Goodison went into raptures.
Everton ended the game looking like a side that deserved to grace Europe as they began show-boating and making Pompey look decidedly ordinary.
Late sub Gary Naysmith added a third for good luck as the Goodison crowd began dreaming of far-flung shores.