Defoe pounced in the 64th minute, seven minutes after Nicolas Anelka had put Chelsea in front with his first Premier League goal since a £15million move from Bolton.
England striker Defoe, a £7million transfer deadline day buy from Tottenham, could even have notched a late winner as Portsmouth came agonisingly close to their first win over Chelsea in 51 years.
Chelsea were again without the injured Frank Lampard and John Terry, while key defender Ricardo Carvalho served a one-match ban.
The visitors still had the better of an entertaining first half and could have taken the lead when Joe Cole's 20-yard curler flew inches wide.
Lassana Diarra began the season at Stamford Bridge and came close to scoring against his old club with a 25-yard pile-driver which goalkeeper Petr Cech did well to stop.
Chelsea were denied in the 34th minute when Michael Ballack's header from a Juliano Belletti corner was cleared off the line by Niko Kranjcar.
The third-placed visitors were saved by the woodwork two minutes later when Noe Pamarot's towering header from a Kranjcar corner smacked against the angle of post and bar.
David James needed all his agility and reactions to save at the feet of Anelka in first-half stoppage time after Florent Malouda delivered a pinpoint pass.
Anelka did not have to wait long and finished brilliantly 11 minutes after the restart after Joe Cole had flicked Malouda's cross into his path.
The goal came seconds after Pompey felt they should have had a penalty for Claude Makelele's obvious looking hand-ball.
Chelsea's hopes of a tenth win in a row were dashed when Defoe took advantage of some slack defending to pick out the bottom right corner after Milan Baros had headed on James' long punt.
Defoe should have won the match 11 minutes from time when he found himself one-on-one with Cech but chipped his shot wide.