Crouch scored in each half to cancel out Leighton Baines' free-kick opener for Everton who produced a below-par performance.
The victory gives Pompey some breathing space at the foot of the Premier League table with crucial fixtures against Bolton and West Brom on the horizon.
Everton struck first inside the opening five minutes when Sylvain Distin's clumsy challenge brought Louis Saha crashing down.
From just outside the 'D' of the 18-yard box, Baines curled in a delightful left-footed free-kick that caught David James off balance to score his first goal in an Everton shirt.
The first half was largely dominated by some sloppy play by both teams, with a number of niggling free-kicks disrupting the flow of the match.
However, Pompey equalised when Sean Davis' corner was only half-cleared allowing Niko Kranjcar to clip a cross towards the far post and find Glen Johnson.
The England full-back's header across goal found Crouch who rose in between Joleon Lescott and Baines to convert.
Portsmouth though nearly undid all their hard work when Sol Campbell inadvertently directed Lars Jacobsen's cross-field pass into the path of Jo but, thankfully for the home side, the Brazilian's radar was wayward and he skewed his effort wide.
The second half opened with Pompey showing greater belief and more attacking intent as David Nugent and Crouch exchanged passes before the former Preston man's low left-footed shot was kept out by the legs of Tim Howard.
Younes Kaboul then troubled the USA international goalkeeper when his cross threatened to sneak in at the near post before Howard parried it to safety.
From the resulting corner, Davis' delivery found Crouch virtually unmarked after he had evaded the attentions of Marouane Fellaini before claiming his third goal in two games.
Pompey were denied a third by the upright when Davis' beautifully struck half-volley rattled off the foot of Howard's far post, but the home side were well worth the win.