The Portuguese centre-back nodded home a 90th-minute leveller in a game in which he had broken the deadlock after just four minutes.
Hooiveld directed home a speculative John Arne Riise drive in the second half and then saw Kieran Richardson's close-range strike brush off him on its way in two minutes from time, although the goal was credited to the Fulham man. However, Fonte saved the Dutchman and his side late on to earn Southampton a fourth point of the campaign.
Southampton had their second corner by the fourth minute and made their early dominance count. Adam Lallana floated the set-piece in from the left and Fonte's glanced header at the near post looped over goalkeeper Mark Schwarzer and into the far corner.
Saints were looking dangerous and came agonisingly close to doubling their advantage as Jay Rodriguez beat the offside trap and pulled back for Rickie Lambert, whose right-footed effort just went wide.
The home side continued to press and Jason Puncheon twice came close from 22nd-minute corners. Puncheon was denied on the goal-line by Sascha Riether and then, from the following corner, the wide man was adjudged to have fouled Schwarzer prior to prodding home.
Paulo Gazzaniga did terrifically to push a close-range Hugo Rodallega header away moments after Steve Sidwell bundled the ball onto the post. Fulham could have also been awarded a penalty after Maya Yoshida appeared to handle in the midst of the action.
Both sides made changes in a bid to change the match but it was an earlier substitute whose impact was felt on the south coast. Riise drilled a low shot from the left and centre-back Hooiveld could only direct it into his own goal, putting Fulham level in the 69th minute.
Rodriguez nodded wide for the hosts in stoppage time and Saints paid when Richardson fired home off Hooiveld's leg two minutes from time.
The substitute looked to have earned Fulham three points but he gave away a late free-kick from which Fonte headed home to earn Saints a point.
Source: PA
Source: PA