The Robins boss was left furious by a 1-0 defeat at Dagenham at the weekend but his side were able to avoid a double Essex defeat by securing a well deserved win at Roots Hall to move up to third in the League Two table.
Marlon Pack put them ahead from the penalty spot and Paul Benson added a second before half-time.
Ben Reeves' late consolation for the home said failed to ruin Yates' night.
"We performed heroically on the whole and I thought we thoroughly deserved our win," he said.
"The players knew I was disappointed with Saturday and I wanted the reaction we got.
"There was energy and desire and we started off very positively which put us in a great position.
"It is an excellent three points for us because Southend is not an easy place to come to and this shows where we want to be at the end of the season."
- Sports & Recreation