Sao Paulo, who won the last three Brazilian league titles under Ramalho, lost for the first time in 10 matches, their surge into the top four in the standings halted in a 1-0 defeat away to Atletico Paranaense on Sunday.
Surprise team Goias are in second place following a 2-1 home win over Santos, while promoted Avai beat Flamengo 3-0 to go 11 matches unbeaten and climb into the top four.
Striker Obina put Palmeiras ahead five minutes before halftime of their match on Saturday with a penalty after playmaker Diego Souza was brought down.
Souza had a part in the second goal when his shot took a rebound and fell to Paraguayan Jose Ortigoza, who scored. Inter pulled one back through Giuliano.
"When you don't have time to improve in training, you have to strengthen the lads in the psychological aspect," Ramalho said referring to Palmeiras' run of three draws and a defeat and the regular pattern of two league matches per week.
"What was most missing was the emotional part. We beat a great team, one of the best in Brazil," he told reporters.
Palmeiras have 40 points from 21 matches, Goias 38, Sao Paulo 36, Avai 34 and Inter, who have two games in hand, 33.
LATE WINNER
Sao Paulo had won their previous seven matches, the best run of any team in the championship, and created more chances but were stunned by 35-year-old Paulo Baier's goal three minutes from time.
The midfielder set off from inside the home side's half, played a one-two with Gabriel and scored with a header.
"In a moment when we dropped our guard they scored," was Sao Paulo defender Miranda's rueful comment.
Referee Arilson Bispo da Anunciacao was criticized by both teams after Corinthians drew 3-3 at home with Botafogo.
The home players complained that, when they were 2-1 up, striker Andre Lima slipped going for Alessandro's cross and used his left hand to help the ball into the net for the equaliser, something television replays appeared to confirm.
Shortly afterwards, Corinthians were lucky to be given a penalty when striker Jorge Henrique dived in the box. Dentinho converted it for his second goal of the match.
Fluminense, Libertadores Cup runners-up little more than a year ago, dropped to the bottom of the standings after a 0-0 draw with Barueri, who had two players sent off in the last 19 minutes.
