Third-placed Milan remain 11 points behind leaders Inter Milan, who warmed up for Tuesday's Champions League clash against Manchester United with a 2-1 win at Bologna on Saturday.
Romanian striker Adrian Mutu hit a stoppage-time winner for Fiorentina who came from behind to beat Chievo Verona 2-1 and moved up to fourth place.
Cagliari, who had won five of their last six games, gave a lively showing at the San Siro against a Milan side that had Filippo Inzaghi alone up front due to injuries to strikers Andriy Shevchenko, Marco Borriello, Ronaldinho and Alexandre Pato, as well as playmaker Kaka.
Inzaghi, who had a goal disallowed for offside in the 22nd minute, was often too isolated and the hosts struggled to create chances in the first half.
David Beckham, back in Milan's starting lineup after sitting out almost all of Wednesday's 1-1 draw at Werder Bremen in the UEFA Cup with a knock, whipped in some nice crosses that went begging.
At the other end Milan keeper Christian Abbiati saved well from Robert Acquafresca (twice) and Andrea Cossu, who then gave the home crowd a scare after the break when he hit the post with a powerful right-footed shot.
Seedorf's goal settled Milan's nerves, although TV replays suggested Lopez may have been given a shove by Inzaghi before tangling with Marchetti.
"It was a difficult game because we have a major emergency in attack at the moment," coach Carlo Ancelotti told Sky television.
"We did very well, considering what was possible. We took the winning chance and hung on until the end. We couldn't do anything else."
Fiorentina's victory over second-from-bottom Chievo finished with skirmishes on the field as the visitors were angry that Mutu scored while one of their players was down hurt.
Chievo went ahead in the 13th minute with a goal by defender Santiago Morero and had midfielder Vincenzo Italiano sent off for a second yellow card in the 82nd. Alberto Gilardino had headed Fiorentina level 17 minutes from time.
Genoa returned to fifth place with a 1-0 win at Napoli thanks to a goal by second-half substitute Bosko Jankovic, and pushed AS Roma, 1-0 victors over Siena on Saturday, back down to sixth in the process.
Second-placed Juventus are nine points behind Inter after they beat Palermo 2-0 on Saturday.
